4WHX | pdb_00004whx

X-ray Crystal Structure of an Amino Acid Aminotransferase from Burkholderia pseudomallei Bound to the Co-factor Pyridoxal Phosphate

• PDB DOI: https://doi.org/10.2210/pdb4WHX/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia pseudomallei 576
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-23 Released: 2014-10-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Fairman, J.W., Dranow, D.M., Taylor, B.M., Lorimer, D., Edwards, T.E.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

X-ray Crystal Structure of an Amino Acid Aminotransferase from Burkholderia pseudomallei Bound to the Co-factor Pyridoxal Phosphate

SSGCID, Fairman, J.W., Dranow, D.M., Taylor, B.M., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 207.83 kDa 
• Atom Count: 15,184 
• Modeled Residue Count: 1,836 
• Deposited Residue Count: 1,866 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain-amino-acid transaminase	A, B, C, D, E, F	311	Burkholderia pseudomallei 576	Mutation(s): 0  Gene Names: ilvE, BUC_1039 EC: 2.6.1.42

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ALA	G [auth A], I [auth C], J [auth D], K [auth E]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
EDO	H [auth A], L [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D, E, F	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34WHX

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.14	α = 90
b = 230.35	β = 90
c = 77.53	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Fairman, J.W., Dranow, D.M., Taylor, B.M., Lorimer, D., Edwards, T.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Structure summary
• Version 2.0: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2019-12-11
  Changes: Author supporting evidence
• Version 2.2: 2023-12-27
  Changes: Data collection, Database references, Refinement description