2NN4 | pdb_00002nn4

Crystal structure of Bacillus subtilis yqgQ, Pfam DUF910

• PDB DOI: https://doi.org/10.2210/pdb2NN4/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-23 Released: 2006-10-31 
• Deposition Author(s): Damodharan, L., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Literature

Structure of YqgQ protein from Bacillus subtilis, a conserved hypothetical protein.

Lakshminarasimhan, D., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 8-11

• PubMed: 20057058 
• DOI: https://doi.org/10.1107/S1744309109047009
• Primary Citation Related Structures: 
  2NN4


• PubMed Abstract: 
  

  The crystal structure of the hypothetical protein YqgQ from Bacillus subtilis has been determined to 2.1 A resolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 51.85, b = 41.25, c = 55.18 A, beta = 113.4 degrees , and contained three protein molecules in the asymmetric unit. The structure was determined by the single-wavelength anomalous dispersion method using selenium-labeled protein and was refined to a final R factor of 24.7% (R(free) = 28.0%). The protein molecule mainly comprises a three-helical bundle. Its putative function is inferred to be single-stranded nucleic acid binding based on sequence and structural homology.

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Organizational Affiliation: 
• Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.11 kDa 
• Atom Count: 1,637 
• Modeled Residue Count: 186 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein yqgQ	A, B, C	72	Bacillus subtilis	Mutation(s): 0  Gene Names: yqgQ
UniProt
Find proteins for P54494 (Bacillus subtilis (strain 168)) Explore P54494  Go to UniProtKB:  P54494

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.85	α = 90
b = 41.25	β = 113.39
c = 55.18	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-31 
Deposition Author(s): Damodharan, L., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-10-31
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-10-24
  Changes: Database references
• Version 1.4: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references