3CMB | pdb_00003cmb

Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution

PDB DOI: https://doi.org/10.2210/pdb3CMB/pdb

Classification: LYASE
Organism(s): Methanoculleus marisnigri JR1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-03-21 Released: 2008-04-01
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.228 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 131.49 kDa
Atom Count: 10,029
Modeled Residue Count: 1,062
Deposited Residue Count: 1,132
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetoacetate decarboxylase	A, B, C, D	283	Methanoculleus marisnigri JR1	Mutation(s): 0 Gene Names: YP_001047042.1, Memar_1128
UniProt
Find proteins for A3CUL0 (Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1)) Explore A3CUL0 Go to UniProtKB: A3CUL0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3CUL0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE8 Query on PE8 Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain Z [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain Z [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain Z [auth C]	FA [auth D], Z [auth C]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain Z [auth C]
P33 Query on P33 Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain I [auth A] MOL2 format, chain T [auth B] MOL2 format, chain I [auth A] mmCIF format, chain T [auth B] mmCIF format, chain I [auth A]	I [auth A], T [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain T [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain N [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain N [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain N [auth A]	AA [auth C] GA [auth D] J [auth A] K [auth A] L [auth A] AA [auth C], GA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], U [auth B], V [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B] Focus chain V [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain H [auth A] SDF format, chain Y [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain Y [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain Y [auth C]	DA [auth D], EA [auth D], H [auth A], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain F [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A]	BA [auth D] CA [auth D] E [auth A] F [auth A] G [auth A] BA [auth D], CA [auth D], E [auth A], F [auth A], G [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], W [auth C], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.228 (Depositor), 0.230 (DCC)
R-Value Observed: 0.229 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33CMB

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.34	α = 90
b = 136.71	β = 90
c = 168.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-04-01

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-04-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary