6G1F

Crystal structure of D-phenylglycine aninotransferase (D-PhgAT) from Pseudomonas stutzeri with PLP internal aldimine

PDB DOI: https://doi.org/10.2210/pdb6G1F/pdb

Classification: TRANSFERASE
Organism(s): Stutzerimonas stutzeri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-03-21 Released: 2019-04-10
Deposition Author(s): Serpico, A., Marles-Wright, J., Campopiano, D.J.
Funding Organization(s): IBioIC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.211
R-Value Work: 0.183
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

D-Phenylglycine aminotransferase (D-PhgAT) – substrate scope and structural insights of a stereo-inverting biocatalyst used in the preparation of aromatic amino acids

Serpico, A., De Cesare, S., Marles-Wright, J., Kalim Akhtar, M., Loake, G.J., Campopiano, D.J.

(2020) Catal Sci Technol

DOI: https://doi.org/10.1039/D0CY01391A

Macromolecule Content

Total Structure Weight: 303.22 kDa
Atom Count: 20,642
Modelled Residue Count: 2,641
Deposited Residue Count: 2,784
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, B, C, D, E A, B, C, D, E, F	464	Stutzerimonas stutzeri	Mutation(s): 0 Gene Names: dpgA
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

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.211
R-Value Work: 0.183
R-Value Observed: 0.184
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.5281/zenodo.1059413

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 329.28	α = 90
b = 83.9	β = 111.58
c = 133.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Marles-Wright, J.

Campopiano, D.J.

Funding Organization	Location	Grant Number
IBioIC	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2020-10-21
Changes: Database references
Version 1.2: 2024-01-17
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.