5VC2

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.199
R-Value Work: 0.165
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5Z9V7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.199
R-Value Work: 0.165
R-Value Observed: 0.166
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-04-26

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.