4O5F | pdb_00004o5f

Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis in complex with pantothenate and phosphate

PDB DOI: https://doi.org/10.2210/pdb4O5F/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia thailandensis E264
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-12-19 Released: 2014-01-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.183 (Depositor), 0.190 (DCC)
R-Value Work:
0.156 (Depositor), 0.170 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis in complex with pantothenate and phosphate

Abendroth, J., Dranow, D.M., Lorimer, D., Fairman, J.W., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 60.72 kDa
Atom Count: 4,454
Modeled Residue Count: 506
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III pantothenate kinase	A, B	280	Burkholderia thailandensis E264	Mutation(s): 0 Gene Names: BTH_I0369, coaX EC: 2.7.1.33
UniProt
Find proteins for Q2T1M2 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T1M2 Go to UniProtKB: Q2T1M2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2T1M2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B]	E [auth A], N [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
PAU Query on PAU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain L [auth B]	C [auth A], L [auth B]	PANTOTHENOIC ACID C₉ H₁₇ N O₅ GHOKWGTUZJEAQD-ZETCQYMHSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B]	D [auth A], M [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B]	H [auth A], I [auth A], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B]	J [auth A], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.183 (Depositor), 0.190 (DCC)
R-Value Work: 0.156 (Depositor), 0.170 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34O5F

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.44	α = 90
b = 99.44	β = 90
c = 112.9	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description