1VK1

Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.165 

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

  • 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

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Conserved hypothetical protein
A
242Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Find proteins for Q8U3S5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U3S5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.148α = 90.00
b = 40.099β = 122.29
c = 65.671γ = 90.00
Software Package:
Software NamePurpose
MolProbitymodel building
SOLVEphasing
SCA2STRUCTUREphasing
SCALEPACKdata scaling
ARP/wARPmodel building
PDB_EXTRACTdata extraction
RESOLVEphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-01-09
    Type: Database references
  • Version 1.4: 2017-10-04
    Type: Refinement description