1VK1

Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.

Shaw, N., Cheng, C., Tempel, W., Chang, J., Ng, J., Wang, X.Y., Perrett, S., Rose, J., Rao, Z., Wang, B.C., Liu, Z.J.

(2007) BMC Struct Biol 7: 46-46

  • DOI: https://doi.org/10.1186/1472-6807-7-46
  • Primary Citation of Related Structures:  
    1VK1

  • PubMed Abstract: 

    The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization

    • Organizational Affiliation: 

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. neilshaw@moon.ibp.ac.cn


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved hypothetical protein242Pyrococcus furiosusMutation(s): 9 
UniProt
Find proteins for Q8U3S5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U3S5 
Go to UniProtKB:  Q8U3S5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U3S5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.148α = 90
b = 40.099β = 122.29
c = 65.671γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
ARP/wARPmodel building
PDB_EXTRACTdata extraction
MolProbitymodel building
SCA2STRUCTUREphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-01-09
    Changes: Database references
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations