1VSF

ASV INTEGRASE CORE DOMAIN WITH MN(II) COFACTOR AND HEPES LIGAND, HIGH MG CONCENTRATION FORM

• PDB DOI: https://doi.org/10.2210/pdb1VSF/pdb

• Classification: ENDORIBONUCLEASE
• Organism(s): Rous sarcoma virus (strain Schmidt-Ruppin)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-11-29 Released: 1996-04-03 
• Deposition Author(s): Bujacz, G., Jaskolski, M., Alexandratos, J., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.189 
• R-Value Observed: 0.130 

Literature

The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations.

Bujacz, G., Jaskolski, M., Alexandratos, J., Wlodawer, A., Merkel, G., Katz, R.A., Skalka, A.M.

(1996) Structure 4: 89-96

• PubMed: 8805516 
• DOI: https://doi.org/10.1016/s0969-2126(96)00012-3
• Primary Citation of Related Structures:  
  1VSD, 1VSE, 1VSF


• PubMed Abstract: 
  

  Members of the structurally-related superfamily of enzymes that includes RNase H, RuvC resolvase, MuA transposase, and retroviral integrase require divalent cations for enzymatic activity. So far, cation positions are reported in the X-ray crystal structures of only two of these proteins, E. coli and human immunodeficiency virus 1 (HIV-1) RNase H. Details of the placement of metal ions in the active site of retroviral integrases are necessary for the understanding of the catalytic mechanism of these enzymes.

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Organizational Affiliation: 

Macromolecular Structure Laboratory, NCI-Frederick Cancer Research and Development Center, ABL-Basic Research Program, Frederick, MD 21702, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.02 kDa 
• Atom Count: 1,281 
• Modelled Residue Count: 146 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTEGRASE	A	152	Rous sarcoma virus (strain Schmidt-Ruppin)	Mutation(s): 0
UniProt
Find proteins for O92956 (Rous sarcoma virus subgroup B (strain Schmidt-Ruppin)) Explore O92956  Go to UniProtKB:  O92956

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.189 
• R-Value Observed: 0.130 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.24	α = 90
b = 66.24	β = 90
c = 81.6	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-04-03 
Deposition Author(s): Bujacz, G., Jaskolski, M., Alexandratos, J., Wlodawer, A.

Revision History  

• Version 1.0: 1996-04-03
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other