1A5T | pdb_00001a5t

CRYSTAL STRUCTURE OF THE DELTA PRIME SUBUNIT OF THE CLAMP-LOADER COMPLEX OF ESCHERICHIA COLI DNA POLYMERASE III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.265 (Depositor) 
  • R-Value Work: 
    0.205 (Depositor) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III.

Guenther, B.Onrust, R.Sali, A.O'Donnell, M.Kuriyan, J.

(1997) Cell 91: 335-345

  • DOI: https://doi.org/10.1016/s0092-8674(00)80417-1
  • Primary Citation Related Structures: 
    1A5T

  • PubMed Abstract: 

    The crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III has been determined. Three consecutive domains in the structure are arranged in a C-shaped architecture. The N-terminal domain contains a nonfunctional nucleotide binding site. The catalytic component of the clamp-loader complex is the gamma subunit, which is homologous to delta'. A sequence-structure alignment suggests that nucleotides bind to gamma at an interdomain interface within the inner surface of the "C." The alignment is extended to other clamp-loader complexes and to the RuvB family of DNA helicases, and suggests that each of these is assembled from C-shaped components that can open and close the jaws of the "C" in response to ATP binding and hydrolysis.


  • Organizational Affiliation
    • The Rockefeller University, New York, New York 10021, USA.

Macromolecule Content 

  • Total Structure Weight: 37.05 kDa 
  • Atom Count: 2,715 
  • Modeled Residue Count: 324 
  • Deposited Residue Count: 334 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DELTA PRIME334Escherichia coli K-12Mutation(s): 0 
Gene Names: HOLB
EC: 2.7.7.7
UniProt
Find proteins for P28631 (Escherichia coli (strain K12))
Explore P28631 
Go to UniProtKB:  P28631
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28631
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.265 (Depositor) 
  • R-Value Work:  0.205 (Depositor) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.9α = 90
b = 104β = 90
c = 75.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    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, Other