3D79 | pdb_00003d79

Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3

PDB DOI: https://doi.org/10.2210/pdb3D79/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Pyrococcus horikoshii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-20 Released: 2008-12-09
Deposition Author(s): Nishimura, Y., Miyazono, K., Sawano, Y., Makino, T., Nagata, K., Tanokura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.229 (Depositor), 0.232 (DCC)
R-Value Work:
0.207 (Depositor), 0.207 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3D79

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

Literature

Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3.

Miyazono, K., Nishimura, Y., Sawano, Y., Makino, T., Tanokura, M.

(2008) Proteins 73: 1068-1071

PubMed: 18831030 Search on PubMed
DOI: https://doi.org/10.1002/prot.22231
Primary Citation Related Structures:
3D79

Organizational Affiliation

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo 113-8657, Japan.

Macromolecule Content

Total Structure Weight: 20.45 kDa
Atom Count: 1,513
Modeled Residue Count: 167
Deposited Residue Count: 179
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH0734	A	179	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH0734.1
UniProt
Find proteins for O58465 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58465 Go to UniProtKB: O58465
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58465
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.229 (Depositor), 0.232 (DCC)
R-Value Work: 0.207 (Depositor), 0.207 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.921	α = 90
b = 52.921	β = 90
c = 133.313	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-12-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references

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.