1WU7 | pdb_00001wu7

Crystal structure of histidyl-tRNA synthetase from Thermoplasma acidophilum

PDB DOI: https://doi.org/10.2210/pdb1WU7/pdb

Classification: LIGASE
Organism(s): Thermoplasma acidophilum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-12-01 Released: 2005-12-06
Deposition Author(s): Tanaka, Y., Sakai, N., Yao, M., Watanabe, N., Tamura, T., Tanaka, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.263 (Depositor), 0.262 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1WU7

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of histidyl-tRNA synthetase from Thermoplasma acidophilum

Tanaka, Y., Sakai, N., Yao, M., Watanabe, N., Tamura, T., Tanaka, I.

To be published.

Macromolecule Content

Total Structure Weight: 100.03 kDa
Atom Count: 6,955
Modeled Residue Count: 844
Deposited Residue Count: 868
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidyl-tRNA synthetase	A, B	434	Thermoplasma acidophilum	Mutation(s): 14 Gene Names: hisS EC: 6.1.1.21
UniProt
Find proteins for Q9HLX5 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HLX5 Go to UniProtKB: Q9HLX5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HLX5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.263 (Depositor), 0.262 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.696	α = 90
b = 101.734	β = 90
c = 167.23	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-12-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-12-06
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.