3EZ4 | pdb_00003ez4

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3EZ4/pdb

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


• Deposited: 2008-10-22 Released: 2008-11-04 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei

Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content 

• Total Structure Weight: 286.04 kDa 
• Atom Count: 19,382 
• Modeled Residue Count: 2,433 
• Deposited Residue Count: 2,690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-methyl-2-oxobutanoate hydroxymethyltransferase	A, B, C, D, E, F, G, H, I, J	269	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: 721, 76, 808, BPSL2824, panB EC: 2.1.2.11
UniProt
Find proteins for Q3JP15 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JP15  Go to UniProtKB:  Q3JP15

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	K [auth E], L [auth F], M [auth G], N [auth H], O [auth I]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.784	α = 90
b = 187.556	β = 90
c = 83.493	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-04 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2008-11-04
  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: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description