1X25 | pdb_00001x25

Crystal Structure of a Member of YjgF Family from Sulfolobus Tokodaii (ST0811)

PDB DOI: https://doi.org/10.2210/pdb1X25/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-04-20 Released: 2006-02-07
Deposition Author(s): Miyakawa, T., Lee, W.C., Hatano, K., Kato, Y., Sawano, Y., Miyazono, K., Nagata, K., Tanokura, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.188 (Depositor), 0.189 (DCC)
R-Value Work:
0.146 (Depositor), 0.149 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the YjgF/YER057c/UK114 family protein from the hyperthermophilic archaeon Sulfolobus tokodaii strain 7

Miyakawa, T., Lee, W.C., Hatano, K., Kato, Y., Sawano, Y., Miyazono, K., Nagata, K., Tanokura, M.

(2006) Proteins 62: 557-561

PubMed: 16323205 Search on PubMed
DOI: https://doi.org/10.1002/prot.20778
Primary Citation Related Structures:
1X25

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 28.31 kDa
Atom Count: 2,189
Modeled Residue Count: 254
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical UPF0076 protein ST0811	A, B	128	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 Gene Names: ST0811
UniProt
Find proteins for Q973T6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q973T6 Go to UniProtKB: Q973T6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q973T6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.188 (Depositor), 0.189 (DCC)
R-Value Work: 0.146 (Depositor), 0.149 (DCC)
R-Value Observed: 0.148 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.98	α = 90
b = 54.98	β = 90
c = 221.557	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-02-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-02-07
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Refinement description

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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.