1XD7 | pdb_00001xd7

Crystal structure of a putative DNA binding protein

• PDB DOI: https://doi.org/10.2210/pdb1XD7/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-04 Released: 2004-09-21 
• Deposition Author(s): Agarwal, R., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.285 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Literature

Crystal structure of a putative DNA binding protein

Agarwal, R., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 16.19 kDa 
• Atom Count: 894 
• Modeled Residue Count: 116 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ywnA	A	145	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: ywnA
UniProt
Find proteins for P71036 (Bacillus subtilis (strain 168)) Explore P71036  Go to UniProtKB:  P71036

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.285 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.892	α = 90
b = 49.362	β = 121.61
c = 51.51	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Agarwal, R., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-09-21
  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: 2019-01-16
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references