2YXY

Crystarl structure of Hypothetical conserved protein, GK0453

• PDB DOI: https://doi.org/10.2210/pdb2YXY/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-27 Released: 2007-10-30 
• Deposition Author(s): Nakamu, Y., Bessho, Y., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Starting Model: experimental

Literature

Structure of the hypothetical DUF1811-family protein GK0453 from Geobacillus kaustophilus HTA426

Padmanabhan, B., Nakamura, Y., Antonyuk, S.V., Strange, R.W., Hasnain, S.S., Yokoyama, S., Bessho, Y.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 342-345

• PubMed: 23545635 
• DOI: https://doi.org/10.1107/S1744309113003369
• Primary Citation of Related Structures:  
  2YXY


• PubMed Abstract: 
  

  The crystal structure of a conserved hypothetical protein, GK0453, from Geobacillus kaustophilus has been determined to 2.2 Å resolution. The crystal belonged to space group P4(3)2(1)2, with unit-cell parameters a = b = 75.69, c = 64.18 Å. The structure was determined by the molecular-replacement method and was refined to a final R factor of 22.6% (R(free) = 26.3%). Based on structural homology, the GK0453 protein possesses two independent binding sites and hence it may simultaneously interact with two proteins or with a protein and a nucleic acid.

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Organizational Affiliation: 

Department of Biophysics, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 13.3 kDa 
• Atom Count: 1,021 
• Modelled Residue Count: 104 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical conserved protein, GK0453	A	115	Geobacillus kaustophilus HTA426	Mutation(s): 0
UniProt
Find proteins for Q5L2U2 (Geobacillus kaustophilus (strain HTA426)) Explore Q5L2U2  Go to UniProtKB:  Q5L2U2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.689	α = 90
b = 75.689	β = 90
c = 64.18	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345dtb	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Nakamu, Y., Bessho, Y., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2013-04-17
  Changes: Database references
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description