4H2P | pdb_00004h2p

Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO)

PDB DOI: https://doi.org/10.2210/pdb4H2P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mesorhizobium japonicum MAFF 303099
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-13 Released: 2013-09-18
Deposition Author(s): Kobayashi, J., Yoshida, H., Mikami, B., Hayashi, H., Kamitori, S., Yagi, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase

Kobayashi, J., Yoshida, H., Mikami, B., Hayashi, H., Kamitori, S., Yagi, T.

To be published.

Macromolecule Content

Total Structure Weight: 178.18 kDa
Atom Count: 13,768
Modeled Residue Count: 1,481
Deposited Residue Count: 1,516
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase	A, B, C, D	379	Mesorhizobium japonicum MAFF 303099	Mutation(s): 0 Gene Names: mlr6788 EC: 1.14.12.4
UniProt
Find proteins for Q988D3 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q988D3 Go to UniProtKB: Q988D3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q988D3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain ZB [auth D] SDF format, chain X [auth B] SDF format, chain E [auth A] SDF format, chain BB [auth C] MOL2 format, chain ZB [auth D] MOL2 format, chain X [auth B] MOL2 format, chain E [auth A] MOL2 format, chain BB [auth C] mmCIF format, chain ZB [auth D] mmCIF format, chain X [auth B] mmCIF format, chain E [auth A] mmCIF format, chain BB [auth C]	BB [auth C], E [auth A], X [auth B], ZB [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain BB [auth C] Focus chain E [auth A] Focus chain X [auth B] Focus chain ZB [auth D] Interactions & Density Focus chain BB [auth C] Focus chain E [auth A] Focus chain X [auth B] Focus chain ZB [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain YB [auth C] SDF format, chain XC [auth D] SDF format, chain AB [auth B] MOL2 format, chain YB [auth C] MOL2 format, chain XC [auth D] MOL2 format, chain AB [auth B] mmCIF format, chain YB [auth C] mmCIF format, chain XC [auth D] mmCIF format, chain AB [auth B]	AB [auth B], XC [auth D], YB [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain XC [auth D] Focus chain YB [auth C] Interactions & Density Focus chain AB [auth B] Focus chain XC [auth D] Focus chain YB [auth C]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain ZA [auth B] SDF format, chain W [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain W [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain W [auth A]	W [auth A], ZA [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain W [auth A] Focus chain ZA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain YA [auth B] SDF format, chain XB [auth C] SDF format, chain XA [auth B] SDF format, chain WC [auth D] SDF format, chain WB [auth C] SDF format, chain WA [auth B] SDF format, chain VC [auth D] SDF format, chain VB [auth C] SDF format, chain VA [auth B] SDF format, chain V [auth A] SDF format, chain UC [auth D] SDF format, chain UB [auth C] SDF format, chain UA [auth B] SDF format, chain U [auth A] SDF format, chain TB [auth C] SDF format, chain TA [auth B] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain XB [auth C] MOL2 format, chain XA [auth B] MOL2 format, chain WC [auth D] MOL2 format, chain WB [auth C] MOL2 format, chain WA [auth B] MOL2 format, chain VC [auth D] MOL2 format, chain VB [auth C] MOL2 format, chain VA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain UC [auth D] MOL2 format, chain UB [auth C] MOL2 format, chain UA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain TB [auth C] MOL2 format, chain TA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain XB [auth C] mmCIF format, chain XA [auth B] mmCIF format, chain WC [auth D] mmCIF format, chain WB [auth C] mmCIF format, chain WA [auth B] mmCIF format, chain VC [auth D] mmCIF format, chain VB [auth C] mmCIF format, chain VA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain UC [auth D] mmCIF format, chain UB [auth C] mmCIF format, chain UA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain TB [auth C] mmCIF format, chain TA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A]	Q [auth A] R [auth A] RA [auth B] S [auth A] SA [auth B] Q [auth A], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], TB [auth C], U [auth A], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], VC [auth D], WA [auth B], WB [auth C], WC [auth D], XA [auth B], XB [auth C], YA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain VC [auth D] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain WC [auth D] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain YA [auth B] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain VC [auth D] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain WC [auth D] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain YA [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FB [auth C] SDF format, chain EC [auth D] SDF format, chain EB [auth C] SDF format, chain DC [auth D] SDF format, chain DB [auth C] SDF format, chain CC [auth D] SDF format, chain BC [auth D] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain EC [auth D] MOL2 format, chain EB [auth C] MOL2 format, chain DC [auth D] MOL2 format, chain DB [auth C] MOL2 format, chain CC [auth D] MOL2 format, chain BC [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain EC [auth D] mmCIF format, chain EB [auth C] mmCIF format, chain DC [auth D] mmCIF format, chain DB [auth C] mmCIF format, chain CC [auth D] mmCIF format, chain BC [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] BC [auth D] CC [auth D] DB [auth C] AA [auth B], BA [auth B], BC [auth D], CC [auth D], DB [auth C], DC [auth D], EB [auth C], EC [auth D], FB [auth C], G [auth A], H [auth A], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BC [auth D] Focus chain CC [auth D] Focus chain DB [auth C] Focus chain DC [auth D] Focus chain EB [auth C] Focus chain EC [auth D] Focus chain FB [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain BC [auth D] Focus chain CC [auth D] Focus chain DB [auth C] Focus chain DC [auth D] Focus chain EB [auth C] Focus chain EC [auth D] Focus chain FB [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain Z [auth B]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain F [auth A] SDF format, chain CB [auth C] SDF format, chain AC [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain F [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain AC [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain F [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain AC [auth D]	AC [auth D], CB [auth C], F [auth A], Y [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain AC [auth D] Focus chain CB [auth C] Focus chain F [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AC [auth D] Focus chain CB [auth C] Focus chain F [auth A] Focus chain Y [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain TC [auth D] SDF format, chain SC [auth D] SDF format, chain SB [auth C] SDF format, chain RC [auth D] SDF format, chain RB [auth C] SDF format, chain QC [auth D] SDF format, chain QB [auth C] SDF format, chain QA [auth B] SDF format, chain PC [auth D] SDF format, chain PB [auth C] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OC [auth D] SDF format, chain OB [auth C] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NC [auth D] SDF format, chain NB [auth C] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MC [auth D] SDF format, chain MB [auth C] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LC [auth D] SDF format, chain LB [auth C] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KC [auth D] SDF format, chain KB [auth C] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JC [auth D] SDF format, chain JB [auth C] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IC [auth D] SDF format, chain IB [auth C] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HC [auth D] SDF format, chain HB [auth C] SDF format, chain HA [auth B] SDF format, chain GC [auth D] SDF format, chain GB [auth C] SDF format, chain GA [auth B] SDF format, chain FC [auth D] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] MOL2 format, chain TC [auth D] MOL2 format, chain SC [auth D] MOL2 format, chain SB [auth C] MOL2 format, chain RC [auth D] MOL2 format, chain RB [auth C] MOL2 format, chain QC [auth D] MOL2 format, chain QB [auth C] MOL2 format, chain QA [auth B] MOL2 format, chain PC [auth D] MOL2 format, chain PB [auth C] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OC [auth D] MOL2 format, chain OB [auth C] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NC [auth D] MOL2 format, chain NB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MC [auth D] MOL2 format, chain MB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LC [auth D] MOL2 format, chain LB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KC [auth D] MOL2 format, chain KB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JC [auth D] MOL2 format, chain JB [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IC [auth D] MOL2 format, chain IB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HC [auth D] MOL2 format, chain HB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain GC [auth D] MOL2 format, chain GB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain FC [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain TC [auth D] mmCIF format, chain SC [auth D] mmCIF format, chain SB [auth C] mmCIF format, chain RC [auth D] mmCIF format, chain RB [auth C] mmCIF format, chain QC [auth D] mmCIF format, chain QB [auth C] mmCIF format, chain QA [auth B] mmCIF format, chain PC [auth D] mmCIF format, chain PB [auth C] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OC [auth D] mmCIF format, chain OB [auth C] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NC [auth D] mmCIF format, chain NB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MC [auth D] mmCIF format, chain MB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LC [auth D] mmCIF format, chain LB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KC [auth D] mmCIF format, chain KB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JC [auth D] mmCIF format, chain JB [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IC [auth D] mmCIF format, chain IB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HC [auth D] mmCIF format, chain HB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain GC [auth D] mmCIF format, chain GB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain FC [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B]	CA [auth B] DA [auth B] EA [auth B] FA [auth B] FC [auth D] CA [auth B], DA [auth B], EA [auth B], FA [auth B], FC [auth D], GA [auth B], GB [auth C], GC [auth D], HA [auth B], HB [auth C], HC [auth D], I [auth A], IA [auth B], IB [auth C], IC [auth D], J [auth A], JA [auth B], JB [auth C], JC [auth D], K [auth A], KA [auth B], KB [auth C], KC [auth D], L [auth A], LA [auth B], LB [auth C], LC [auth D], M [auth A], MA [auth B], MB [auth C], MC [auth D], N [auth A], NA [auth B], NB [auth C], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], QA [auth B], QB [auth C], QC [auth D], RB [auth C], RC [auth D], SB [auth C], SC [auth D], TC [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FC [auth D] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth D] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain HC [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain RB [auth C] Focus chain RC [auth D] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain TC [auth D] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FC [auth D] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth D] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain HC [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain RB [auth C] Focus chain RC [auth D] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain TC [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.838	α = 90
b = 103.838	β = 90
c = 452.781	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description