5VC2 | pdb_00005vc2

Crystal structure of a serine hydroxymethyltransferase from Helicobacter pylori

• PDB DOI: https://doi.org/10.2210/pdb5VC2/pdb

• Classification: TRANSFERASE
• Organism(s): Helicobacter pylori G27
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-30 Released: 2017-04-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a serine hydroxymethyltransferase from Helicobacter pylori

Edwards, T.E., Mayclin, S.J., Lorimer, D.D., 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.72 kDa 
• Atom Count: 6,479 
• Modeled Residue Count: 766 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B	424	Helicobacter pylori G27	Mutation(s): 0  Gene Names: glyA, HPG27_169 EC: 2.1.2.1
UniProt
Find proteins for B5Z9V7 (Helicobacter pylori (strain G27)) Explore B5Z9V7  Go to UniProtKB:  B5Z9V7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.97	α = 90
b = 91.02	β = 90
c = 161.32	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description