5GHF | pdb_00005ghf

Transaminase with L-ala

PDB DOI: https://doi.org/10.2210/pdb5GHF/pdb

Classification: TRANSFERASE
Organism(s): Brucella anthropi ATCC 49188
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-19 Released: 2017-05-24
Deposition Author(s): Kim, J., Park, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.174 (Depositor), 0.182 (DCC)
R-Value Work:
0.135 (Depositor), 0.148 (DCC)
R-Value Observed:
0.137 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5GHF

Ligand Structure Quality Assessment

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

Literature

Active Site Engineering of omega-Transaminase Guided by Docking Orientation Analysis and Virtual Activity Screening

Han, S.-W., Kim, J., Cho, H.-S., Shin, J.-S.

(2017) ACS Catal 7: 3752-3762

DOI: https://doi.org/10.1021/acscatal.6b03242

Macromolecule Content

Total Structure Weight: 99.91 kDa
Atom Count: 7,526
Modeled Residue Count: 855
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class-III	A, B	456	Brucella anthropi ATCC 49188	Mutation(s): 0 Gene Names: Oant_0199
UniProt
Find proteins for A6WVC6 (Brucella anthropi (strain ATCC 49188 / DSM 6882 / CCUG 24695 / JCM 21032 / LMG 3331 / NBRC 15819 / NCTC 12168 / Alc 37)) Explore A6WVC6 Go to UniProtKB: A6WVC6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6WVC6
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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.174 (Depositor), 0.182 (DCC)
R-Value Work: 0.135 (Depositor), 0.148 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.8	α = 90
b = 102	β = 90
c = 116.73	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-05-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-05-24
Type: Initial release
Version 1.1: 2024-03-20
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.