6THQ | pdb_00006thq

Crystal structure of branched-chain aminotransferase from thermophilic archaea Thermoproteus uzoniensis with norvaline

PDB DOI: https://doi.org/10.2210/pdb6THQ/pdb

Classification: TRANSFERASE
Organism(s): Thermoproteus uzoniensis 768-20
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-11-21 Released: 2020-09-30
Deposition Author(s): Boyko, K.M., Nikolaeva, A.Y., Bezsudnova, E.Y., Popov, V.O.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.234 (Depositor), 0.234 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Three-Dimensional Structure of Branched-Chain Amino Acid Transaminase from Thermoproteus uzoniensis in Complex with L-Norvaline

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

(2020) Crystallogr Rep

Macromolecule Content

Total Structure Weight: 104.67 kDa
Atom Count: 7,304
Modeled Residue Count: 894
Deposited Residue Count: 921
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain-amino-acid aminotransferase	A, B, C	307	Thermoproteus uzoniensis 768-20	Mutation(s): 0 Gene Names: ilvE, TUZN_1299 EC: 2.6.1.42
UniProt
Find proteins for F2L0W0 (Thermoproteus uzoniensis (strain 768-20)) Explore F2L0W0 Go to UniProtKB: F2L0W0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2L0W0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PY5 (Subject of Investigation/LOI) Query on PY5 Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C]	2-[O-PHOSPHONOPYRIDOXYL]-AMINO-PENTANOIC ACID C₁₃ H₂₁ N₂ O₇ P YYAMSLLSQINIQO-NSHDSACASA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C]	D [auth A], F [auth B], H [auth C]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.234 (Depositor), 0.234 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.46	α = 90
b = 93.46	β = 90
c = 213.17	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-30

Deposition Author(s):

Nikolaeva, A.Y.

Bezsudnova, E.Y.

Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	19-14-00164

Revision History (Full details and data files)

Version 1.0: 2020-09-30
Type: Initial release
Version 1.1: 2024-01-24
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.