Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.05 kDa 
• Atom Count: 2715 
• Modelled Residue Count: 324 
• Deposited Residue Count: 334 
• Unique protein chains: 1

1A5T

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

• PDB DOI: 10.2210/pdb1A5T/pdb

• Classification: ZINC FINGER
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-02-18 Released: 1998-05-27 
• Deposition Author(s): Guenther, B., Onrust, R., Sali, A., O'Donnell, M., Kuriyan, J.

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Experimental Data Snapshot

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

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

• PubMed: 9363942 
• DOI: 10.1016/s0092-8674(00)80417-1
• Primary Citation of 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.

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Related Citations: 

• Structural Studies on the DNA Replication Apparatus: X-Ray Crystal Structure of the Delta-Prime Subunit of Escherichia Coli DNA Polymerase III
  Guenther, B.D.
  (1996) Thesis --: --

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Organizational Affiliation: 

The Rockefeller University, New York, New York 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DELTA PRIME	A	334	Escherichia coli K-12	Mutation(s): 0  Gene Names: holB, b1099, JW1085 EC: 2.7.7.7
UniProt
Find proteins for P28631 (Escherichia coli (strain K12)) Explore P28631  Go to UniProtKB:  P28631

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.9	α = 90
b = 104	β = 90
c = 75.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-02-18 
• Released Date: 1998-05-27 
Deposition Author(s): Guenther, B., Onrust, R., Sali, A., O'Donnell, M., Kuriyan, J.

Revision History  

• 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