Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.03 kDa 
• Atom Count: 2702 
• Modelled Residue Count: 341 
• Deposited Residue Count: 354 
• Unique protein chains: 1

1K1S

Crystal Structure of DinB from Sulfolobus solfataricus

• PDB DOI: 10.2210/pdb1K1S/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-09-25 Released: 2001-10-31 
• Deposition Author(s): Silvian, L.F., Toth, E.A., Pham, P., Goodman, M.F., Ellenberger, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.279 
• R-Value Work: 0.237 

Literature

Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus.

Silvian, L.F., Toth, E.A., Pham, P., Goodman, M.F., Ellenberger, T.

(2001) Nat Struct Biol 8: 984-989

• PubMed: 11685247 
• DOI: 10.1038/nsb1101-984
• Primary Citation of Related Structures:  
  1K1Q, 1K1S


• PubMed Abstract: 
  

A new group of error-prone DNA polymerases overcomes the blockage posed to normal DNA replication by damaged template bases, suggesting an active site with a loose, flexible pocket that accommodates aberrant DNA structures. We have determined a 2.8 A resolution crystal structure of the Sulfolobus solfataricus Dbh protein, a DNA translesion polymerase closely related to Escherichia coli DNA polymerase IV and human polymerase kappa. A high error rate is observed for the Dbh polymerase in a range of 10(-2)-10(-3) for all 12 base substitution mispairs. The crystal structure of Dbh reveals an overall architecture resembling other DNA polymerases but has unique features that are likely to contribute to error-prone synthesis, including -1 frameshifting mutations.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DBH protein	A	354	Saccharolobus solfataricus	Mutation(s): 1  Gene Names: DINB, dbh EC: 2.7.7.7
UniProt
Find proteins for P96022 (Saccharolobus solfataricus) Explore P96022  Go to UniProtKB:  P96022

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.279 
• R-Value Work: 0.237 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.04	α = 90
b = 113.04	β = 90
c = 62.58	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-25 
• Released Date: 2001-10-31 
Deposition Author(s): Silvian, L.F., Toth, E.A., Pham, P., Goodman, M.F., Ellenberger, T.

Revision History  

• Version 1.0: 2001-10-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references