6H65 | pdb_00006h65

Crystal structure of the branched-chain-amino-acid aminotransferase from Haliangium ochraceum

PDB DOI: https://doi.org/10.2210/pdb6H65/pdb

Classification: TRANSFERASE
Organism(s): Haliangium ochraceum DSM 14365
Mutation(s): No

Deposited: 2018-07-26 Released: 2018-10-10
Deposition Author(s): Boyko, K.M., Timofeev, V.I., Bezsudnova, E.Y., Nikolaeva, A.Y., Rakitina, T.V., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.199 (Depositor), 0.199 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the branched-chain-amino-acid aminotransferase from Haliangium ochraceum

Boyko, K.M., Timofeev, V.I., Bezsudnova, E.Y., Nikolaeva, A.Y., Rakitina, T.V., Popov, V.O.

To be published.

Macromolecule Content

Total Structure Weight: 215.4 kDa
Atom Count: 14,697
Modeled Residue Count: 1,837
Deposited Residue Count: 1,902
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain-amino-acid aminotransferase	A, B, C, D, E A, B, C, D, E, F	317	Haliangium ochraceum DSM 14365	Mutation(s): 0 EC: 2.6.1.42
UniProt
Find proteins for D0LR31 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2)) Explore D0LR31 Go to UniProtKB: D0LR31
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0LR31
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth E] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.235 (Depositor), 0.235 (DCC)
R-Value Work: 0.199 (Depositor), 0.199 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.08	α = 90
b = 164.93	β = 90
c = 254.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
BALBES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-10-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-10-10
Type: Initial release
Version 1.1: 2025-04-09
Changes: Data collection, Database references, Refinement description, Structure summary

6H65 | pdb_00006h65

Crystal structure of the branched-chain-amino-acid aminotransferase from Haliangium ochraceum

Literature

Crystal structure of the branched-chain-amino-acid aminotransferase from Haliangium ochraceum

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)