2CY8 | pdb_00002cy8

Crystal structure of D-phenylglycine aminotransferase (D-PhgAT) from Pseudomonas strutzeri ST-201

PDB DOI: https://doi.org/10.2210/pdb2CY8/pdb

Classification: TRANSFERASE
Organism(s): Stutzerimonas stutzeri
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-07-05 Released: 2006-09-26
Deposition Author(s): Kongsaeree, P., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.223 (Depositor), 0.230 (DCC)
R-Value Work:
0.184 (Depositor), 0.190 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of D-phenylglycine aminotransferase (D-PhgAT) from Pseudomonas strutzeri ST-201

Kongsaeree, P., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 49.03 kDa
Atom Count: 3,185
Modeled Residue Count: 402
Deposited Residue Count: 453
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-phenylglycine aminotransferase	A	453	Stutzerimonas stutzeri	Mutation(s): 0
UniProt
Find proteins for Q6VY99 (Stutzerimonas stutzeri) Explore Q6VY99 Go to UniProtKB: Q6VY99
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6VY99
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.223 (Depositor), 0.230 (DCC)
R-Value Work: 0.184 (Depositor), 0.190 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.684	α = 90
b = 74.684	β = 90
c = 147.411	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-09-26

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-09-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references

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.