1X25

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.188 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1002/prot.20778
• Primary Citation of Related Structures:  
  1X25

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 generated by PQS (software)

Macromolecule Content

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.188 
• R-Value Work: 0.146 
• R-Value Observed: 0.148 
• 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

Entry History 

Deposition Data

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

Revision History  

• 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