1CXQ

ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM AMMONIUM SULFATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

  • Primary Citation of Related Structures:  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 provid ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AVIAN SARCOMA VIRUS INTEGRASE
A
162Rous sarcoma virus (strain Schmidt-Ruppin B)Gene Names: gag-pro-pol
EC: 3.1.26.4, 3.1.-.-, 2.7.7.49, 2.7.7.7, 2.7.7.-, 3.4.23.-
Find proteins for O92956 (Rous sarcoma virus (strain Schmidt-Ruppin B))
Go to UniProtKB:  O92956
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.130 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.540α = 90.00
b = 65.540β = 90.00
c = 80.120γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
HKL-2000data scaling
X-PLORphasing
MAR345data collection
SHELXLrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description