2P1J

Crystal structure of a polC-type DNA polymerase III exonuclease domain from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb2P1J/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-05 Released: 2007-03-20 
• Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Izuka, M., Sridhar, V., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.298 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 

Literature

Crystal structure of a polC-type DNA polymerase III exonuclease domain from Thermotoga maritima

Bonanno, J.B., Rutter, M., Bain, K.T., Izuka, M., Sridhar, V., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Macromolecule Content

• Total Structure Weight: 42.81 kDa 
• Atom Count: 2,809 
• Modelled Residue Count: 335 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III polC-type	A, B	186	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: polC, TM_0576 EC: 2.7.7.7
UniProt
Find proteins for Q9ZHF6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9ZHF6  Go to UniProtKB:  Q9ZHF6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.298 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.703	α = 90
b = 124.939	β = 90
c = 143.062	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Izuka, M., Sridhar, V., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-03-20
  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: Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.6: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.7: 2024-02-21
  Changes: Data collection, Database references