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 1.4 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: 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


    Related Citations: 
    • Crystal structure solution of a ParB-like nuclease at atomic resolution.
      Shaw, N., Tempel, W., Chang, J., Yang, H., Cheng, C., Ng, J., Rose, J., Rao, Z., Wang, B.C., Liu, Z.J.
      (2008) Proteins 70: 263

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Conserved hypothetical proteinA242Pyrococcus furiosusMutation(s): 9 
Find proteins for Q8U3S5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U3S5 
Go to UniProtKB:  Q8U3S5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
AL-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



Entry History 

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