5LHA

Amine transaminase crystal structure from an uncultivated Pseudomonas species in the PMP-bound form

PDB DOI: https://doi.org/10.2210/pdb5LHA/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-07-10 Released: 2017-03-22
Deposition Author(s): Reddem, E., Thunnissen, A.M.W.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.225
R-Value Work: 0.172
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Explaining Operational Instability of Amine Transaminases: Substrate-Induced Inactivation Mechanism and Influence of Quaternary Structure on Enzyme-Cofactor Intermediate Stability.

Borner, T., Ramisch, S., Reddem, E., Bartsch, S., Vogel, A., Thunnissen, A.M.W.H., Adlercreutz, P., Grey, C.

(2017) ACS Catal 7: 1259-1269

DOI: https://doi.org/10.1021/acscatal.6b02100

Macromolecule Content

Total Structure Weight: 199.27 kDa
Atom Count: 14,339
Modelled Residue Count: 1,786
Deposited Residue Count: 1,832
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OMEGA TRANSAMINASE	A, B, C, D	458	Pseudomonas sp.	Mutation(s): 0 EC: 2.6.1.18
UniProt
Find proteins for A0A1W2VMW5 (Pseudomonas sp) Explore A0A1W2VMW5 Go to UniProtKB: A0A1W2VMW5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1W2VMW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMP Query on PMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.225
R-Value Work: 0.172
R-Value Observed: 0.175
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.79	α = 90
b = 97.069	β = 90
c = 153.389	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Thunnissen, A.M.W.H.

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2024-05-08
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.