1G71 | pdb_00001g71

CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS DNA PRIMASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.249 (Depositor) 
  • R-Value Work: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1G71

This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a DNA-dependent RNA polymerase (DNA primase).

Augustin, M.A.Huber, R.Kaiser, J.T.

(2001) Nat Struct Biol 8: 57-61

  • DOI: https://doi.org/10.1038/83060
  • Primary Citation Related Structures: 
    1G71

  • PubMed Abstract: 

    Primases are essential components of the DNA replication apparatus in every organism. They catalyze the synthesis of oligoribonucleotides on single-stranded DNA, which subsequently serve as primers for the replicative DNA polymerases. In contrast to bacterial primases, the archaeal enzymes are closely related to their eukaryotic counterparts. We have solved the crystal structure of the catalytic primase subunit from the hyperthermophilic archaeon Pyrococcus furiosus at 2.3 A resolution by multiwavelength anomalous dispersion methods. The structure shows a two-domain arrangement with a novel zinc knuckle motif located in the primase (prim) domain. In this first structure of a complete protein of the archaeal/eukaryotic primase family, the arrangement of the catalytically active residues resembles the active sites of various DNA polymerases that are unrelated in fold.


  • Organizational Affiliation
    • Max-Planck-Institut für Biochemie, Abteilung für Strukturforschung, Am Klopferspitz 18A, D-82152 Martinsried, Germany. augustin@biochem.mpg.de

Macromolecule Content 

  • Total Structure Weight: 82.41 kDa 
  • Atom Count: 6,070 
  • Modeled Residue Count: 688 
  • Deposited Residue Count: 694 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA PRIMASE
A, B
347Pyrococcus furiosusMutation(s): 0 
EC: 2.7.7
UniProt
Find proteins for Q9P9H1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q9P9H1 
Go to UniProtKB:  Q9P9H1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P9H1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
M [auth B],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
J [auth B]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.249 (Depositor) 
  • R-Value Work:  0.211 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.883α = 90
b = 136.326β = 90
c = 61.877γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-10
    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: 2024-02-07
    Changes: Data collection, Database references, Derived calculations