3NR6

Crystal structure of xenotropic murine leukemia virus-related virus (XMRV) protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of XMRV protease differs from the structures of other retropepsins.

Li, M.Dimaio, F.Zhou, D.Gustchina, A.Lubkowski, J.Dauter, Z.Baker, D.Wlodawer, A.

(2011) Nat.Struct.Mol.Biol. 18: 227-229

  • DOI: 10.1038/nsmb.1964

  • PubMed Abstract: 
  • Using energy and density guided Rosetta refinement to improve molecular replacement, we determined the crystal structure of the protease encoded by xenotropic murine leukemia virus-related virus (XMRV). Despite overall similarity of XMRV protease to ...

    Using energy and density guided Rosetta refinement to improve molecular replacement, we determined the crystal structure of the protease encoded by xenotropic murine leukemia virus-related virus (XMRV). Despite overall similarity of XMRV protease to other retropepsins, the topology of its dimer interface more closely resembles those of the monomeric, pepsin-like enzymes. Thus, XMRV protease may represent a distinct branch of the aspartic protease family.


    Organizational Affiliation

    Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease p14
A, B
132Xenotropic MuLV-related virusMutation(s): 0 
Gene Names: gag-pol
Find proteins for A1Z651 (Xenotropic MuLV-related virus)
Go to UniProtKB:  A1Z651
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 
  • Space Group: P 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 63.915α = 90.00
b = 63.915β = 90.00
c = 106.509γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
Rosettaphasing
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
REFMACrefinement
Rosettamodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description