1ULY | pdb_00001uly

Crystal structure analysis of the ArsR homologue DNA-binding protein from P. horikoshii OT3

PDB DOI: https://doi.org/10.2210/pdb1ULY/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-09-17 Released: 2004-10-19
Deposition Author(s): Itou, H., Yao, M., Watanabe, N., Tanaka, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.268 (Depositor), 0.270 (DCC)
R-Value Work:
0.204 (Depositor), 0.211 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 1ULY

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the PH1932 protein, a unique archaeal ArsR type winged-HTH transcription factor from Pyrococcus horikoshii OT3

Itou, H., Yao, M., Watanabe, N., Tanaka, I.

(2008) Proteins 70: 1631-1634

PubMed: 18076033 Search on PubMed
DOI: https://doi.org/10.1002/prot.21851
Primary Citation Related Structures:
1ULY

Organizational Affiliation

Frontier Research Center for Post-genomic Science and Technology, Hokkaido University, Sapporo 001-0021, Japan.

Macromolecule Content

Total Structure Weight: 23.08 kDa
Atom Count: 1,605
Modeled Residue Count: 190
Deposited Residue Count: 192
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein PH1932	A	192	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: PH1932
UniProt
Find proteins for O59595 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59595 Go to UniProtKB: O59595
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O59595
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.268 (Depositor), 0.270 (DCC)
R-Value Work: 0.204 (Depositor), 0.211 (DCC)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.64	α = 90
b = 90.64	β = 90
c = 132.26	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-10-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-10-19
Type: Initial release
Version 1.1: 2008-03-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-11-13
Changes: Structure summary

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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.