Experimental Data Snapshot

  • Resolution: 1.42 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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This is version 1.3 of the entry. See complete history


Atomic resolution structures of the core domain of avian sarcoma virus integrase and its D64N mutant.

Lubkowski, J.Dauter, Z.Yang, F.Alexandratos, J.Merkel, G.Skalka, A.M.Wlodawer, A.

(1999) Biochemistry 38: 13512-13522

  • DOI: https://doi.org/10.1021/bi991362q
  • Primary Citation of Related Structures:  
    1CXQ, 1CXU, 1CZ9, 1CZB

  • PubMed Abstract: 

    Six crystal structures of the core domain of integrase (IN) from avian sarcoma virus (ASV) and its active-site derivative containing an Asp64 --> Asn substitution have been solved at atomic resolution ranging 1.02-1.42 A. The high-quality data provide new structural information about the active site of the enzyme and clarify previous inconsistencies in the description of this fragment. The very high resolution of the data and excellent quality of the refined models explain the dynamic properties of IN and the multiple conformations of its disordered residues. They also allow an accurate description of the solvent structure and help to locate other molecules bound to the enzyme. A detailed analysis of the flexible active-site region, in particular the loop formed by residues 144-154, suggests conformational changes which may be associated with substrate binding and enzymatic activity. The pH-dependent conformational changes of the active-site loop correlates with the pH vs activity profile observed for ASV IN.

  • Organizational Affiliation

    Macromolecular Structure Laboratory, National Cancer Institute-Frederick Cancer Research and Development Center (NCI-FCRDC), ABL-Basic Research Program, Maryland 21702, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (AVIAN SARCOMA VIRUS INTEGRASE)162Avian sarcoma virusMutation(s): 0 
Find proteins for O92956 (Rous sarcoma virus subgroup B (strain Schmidt-Ruppin))
Explore O92956 
Go to UniProtKB:  O92956
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO92956
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.42 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.177α = 90
b = 66.177β = 90
c = 78.73γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-09-08
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations