3A2F | pdb_00003a2f

Crystal Structure of Pyrococcus furiosus DNA polymerase/PCNA monomer mutant complex

PDB DOI: https://doi.org/10.2210/pdb3A2F/pdb

Classification: TRANSFERASE/REPLICATION
Organism(s): Pyrococcus furiosus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-05-15 Released: 2009-11-03
Deposition Author(s): Nishida, H., Ishino, Y., Morikawa, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free:
0.284 (Depositor), 0.281 (DCC)
R-Value Work:
0.241 (Depositor), 0.237 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex

Nishida, H., Mayanagi, K., Kiyonari, S., Sato, Y., Ishino, Y., Morikawa, K.

To be published.

Macromolecule Content

Total Structure Weight: 118.9 kDa
Atom Count: 8,254
Modeled Residue Count: 1,020
Deposited Residue Count: 1,023
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	775	Pyrococcus furiosus	Mutation(s): 0 Gene Names: pol, PF0212 EC: 2.7.7.7
UniProt
Find proteins for P61875 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P61875 Go to UniProtKB: P61875
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61875
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase sliding clamp	B	248	Pyrococcus furiosus	Mutation(s): 3 Gene Names: pcn, PF0983
UniProt
Find proteins for O73947 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore O73947 Go to UniProtKB: O73947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O73947
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.284 (Depositor), 0.281 (DCC)
R-Value Work: 0.241 (Depositor), 0.237 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.354	α = 90
b = 90.451	β = 90
c = 186.211	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-11-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2024-11-06
Changes: Data collection, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.