4O8K | pdb_00004o8k

Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis, apo structure

• PDB DOI: https://doi.org/10.2210/pdb4O8K/pdb

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


• Deposited: 2013-12-28 Released: 2014-01-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.186 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis, apo structure

Seattle Structural Genomics Center for Infectious Disease, Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.71 kDa 
• Atom Count: 4,112 
• Modeled Residue Count: 501 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	C [auth A], D [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.186 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34O8K

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.94	α = 90
b = 95.94	β = 90
c = 109.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary