3D7A | pdb_00003d7a

Crystal structure of DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3

PDB DOI: https://doi.org/10.2210/pdb3D7A/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): Shirokane, M., Miyazono, K.I., Sawano, Y., Tanokura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.281 (Depositor), 0.278 (DCC)
R-Value Work:
0.238 (Depositor), 0.236 (DCC)
R-Value Observed:
0.240 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the DUF54 family protein PH1010 from hyperthermophilic archaea Pyrococcus horikoshii OT3.

Miyazono, K.I., Shirokane, M., Sawano, Y., Tanokura, M.

(2008) Proteins 74: 256-260

PubMed: 18831045 Search on PubMed
DOI: https://doi.org/10.1002/prot.22255
Primary Citation Related Structures:
3D7A

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 32.16 kDa
Atom Count: 2,393
Modeled Residue Count: 271
Deposited Residue Count: 276
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0201 protein PH1010	A, B	138	Pyrococcus horikoshii	Mutation(s): 0 Gene Names: PH1010
UniProt
Find proteins for O58738 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58738 Go to UniProtKB: O58738
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O58738
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.281 (Depositor), 0.278 (DCC)
R-Value Work: 0.238 (Depositor), 0.236 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.934	α = 90
b = 49.526	β = 90
c = 132.695	γ = 90

Software Package:

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

Structure Validation

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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: Advisory, Refinement description
Version 1.3: 2024-03-20
Changes: Advisory, Data collection, Database references

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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.