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), 0.228 (DCC)
R-Value Work:
0.184 (Depositor), 0.191 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2CY8

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.228 (DCC)
R-Value Work: 0.184 (Depositor), 0.191 (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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.