2XCD

Structure of YncF,the genomic dUTPase from Bacillus subtilis

Structural Biology Knowledgebase: 2XCD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.155

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2XCD

Classification: HYDROLASE

Total Structure Weight: 98976.31

Macromolecule Entities
Molecule Chains Length Organism Details
PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF A, B, C..., D, E, FA, B, C, D, E, F 144 Bacillus subtilis EC#: 3.6.1.23 IUBMB
Gene Name(s): yncF BSU17660
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

C, E, F CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, E MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, C, D, E, F SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.155
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 98.81 α = 90.00
b = 98.84 β = 90.00
c = 99.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-04-22
  • Released Date: 2010-08-11
  • Deposition author(s): Garcia, J., Burchell, L., Takezawa, M., Rzechorzek, N.J., Fogg, M., Wilson, K.S.

Revision History

  • 2012-04-11
    Type: Citation | Details: JRNL
  • 2012-04-11
    Type: Version format compliance | Details: REMARK 4
  • 2012-04-11
    Type: Non-polymer description | Details: HETSYN