3ECD | pdb_00003ecd

Crystal structure of serine hydroxymethyltransferase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3ECD/pdb

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


• Deposited: 2008-08-29 Released: 2008-09-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.206 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of serine hydroxymethyltransferase from Burkholderia pseudomallei

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 182.72 kDa 
• Atom Count: 13,236 
• Modeled Residue Count: 1,544 
• Deposited Residue Count: 1,700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase 2	A, B, C, D	425	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: glyA2, BPSS0547 EC: 2.1.2.1
UniProt
Find proteins for Q3JGP5 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JGP5  Go to UniProtKB:  Q3JGP5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.206 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.212	α = 97.79
b = 61.865	β = 89.97
c = 117.577	γ = 110.24

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description