5VMB | pdb_00005vmb

Crystal structure of a glycine hydroxymethyltransferase from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb5VMB/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-04-27 Released: 2017-05-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a glycine hydroxymethyltransferase from Acinetobacter baumannii

Edwards, T.E., Abendroth, J., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 46.08 kDa
Atom Count: 2,970
Modeled Residue Count: 401
Deposited Residue Count: 425
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	425	Acinetobacter baumannii	Mutation(s): 0 Gene Names: glyA, glyA2, A7M79_08275, A7M90_04720, A7N09_12635, A8A08_14715, A8G88_00905, AB895_0334, AB988_4249, ABUW_1333... glyA, glyA2, A7M79_08275, A7M90_04720, A7N09_12635, A8A08_14715, A8G88_00905, AB895_0334, AB988_4249, ABUW_1333, APD06_10955, AZE33_14190, BGC29_02480, IX87_07645, LV38_04033 EC: 2.1.2.1
UniProt
Find proteins for V5VBJ2 (Acinetobacter baumannii) Explore V5VBJ2 Go to UniProtKB: V5VBJ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V5VBJ2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.233 (Depositor), 0.230 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.187 (Depositor)

Diffraction Data: https://doi.org/10.18430/M35VMB

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.84	α = 90
b = 95.84	β = 90
c = 109.69	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.