5LHA | pdb_00005lha

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 (Depositor), 0.222 (DCC)
R-Value Work:
0.172 (Depositor), 0.167 (DCC)
R-Value Observed:
0.175 (Depositor)

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Ligand Structure Quality Assessment

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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
Modeled Residue Count: 1,786
Deposited Residue Count: 1,832
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF 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 (Depositor), 0.222 (DCC)
R-Value Work: 0.172 (Depositor), 0.167 (DCC)
R-Value Observed: 0.175 (Depositor)

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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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

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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.