2P1J | pdb_00002p1j

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.298 (Depositor), 0.290 (DCC)
R-Value Work:
0.229 (Depositor), 0.220 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ZHF6
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.298 (Depositor), 0.290 (DCC)
R-Value Work: 0.229 (Depositor), 0.220 (DCC)
R-Value Observed: 0.232 (Depositor)

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-03-20

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.