2DUD | pdb_00002dud

Crystal structure of human mitochondrial single-stranded DNA-binding protein(hmtSSB)

• PDB DOI: https://doi.org/10.2210/pdb2DUD/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2006-07-21 Released: 2007-01-21 
• Deposition Author(s): Dong, X., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.287 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human mitochondrial single-stranded DNA-binding protein(hmtSSB)

Dong, X., Bessho, Y., Shirouzu, M., Yokoyama, 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 (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.71 kDa 
• Atom Count: 1,539 
• Modeled Residue Count: 187 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A, B	133	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q04837 (Homo sapiens) Explore Q04837  Go to UniProtKB:  Q04837
PHAROS:  Q04837 GTEx:  ENSG00000106028

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.287 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.9	α = 90
b = 106.9	β = 90
c = 90.24	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-21 
Deposition Author(s): Dong, X., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-01-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description