1WV9

Crystal Structure of Rhodanese Homolog TT1651 from an Extremely Thermophilic Bacterium Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb1WV9/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-12-12 Released: 2005-06-19
Deposition Author(s): Mizohata, E., Hattori, M., Tatsuguchi, A., Terada, T., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.258 (Depositor), 0.267 (DCC)
R-Value Work:
0.215 (Depositor), 0.219 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8

Hattori, M., Mizohata, E., Tatsuguchi, A., Shibata, R., Kishishita, S., Murayama, K., Terada, T., Kuramitsu, S., Shirouzu, M., Yokoyama, S.

(2006) Proteins 64: 284-287

PubMed: 16680676 Search on PubMed
DOI: https://doi.org/10.1002/prot.20937
Primary Citation of Related Structures:
1WV9

Organizational Affiliation

RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Macromolecule Content

Total Structure Weight: 20.96 kDa
Atom Count: 1,465
Modelled Residue Count: 173
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodanese Homolog TT1651	A, B	94	Thermus thermophilus	Mutation(s): 2
UniProt
Find proteins for Q5SKN0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKN0 Go to UniProtKB: Q5SKN0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SKN0
Sequence Annotations Expand
Reference Sequence LOADING

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: 2.00 Å
R-Value Free: 0.258 (Depositor), 0.267 (DCC)
R-Value Work: 0.215 (Depositor), 0.219 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.218	α = 90
b = 45.218	β = 90
c = 79.51	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-06-19

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2005-06-19
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: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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.