4AOZ

B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121)

Structural Biology Knowledgebase: 4AOZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.159

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AOZ

Classification: HYDROLASE

Total Structure Weight: 50534.39

Macromolecule Entities
Molecule Chains Length Organism Details
PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF A, B, C 144 Bacillus subtilis EC#: 3.6.1.23 IUBMB
Gene Name(s): yncF BSU17660

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ACT
Query on ACT

C ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
CL
Query on CL

C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
DUR
Query on DUR

A, B, C 2'-DEOXYURIDINE
C9 H12 N2 O5
MXHRCPNRJAMMIM-SHYZEUOFSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

B, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
POP
Query on POP

B, C PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.159
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.27 α = 90.00
b = 71.53 β = 90.00
c = 92.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-30
  • Released Date: 2013-05-01
  • Deposition author(s): Timm, J., Garcia-Nafria, J., Harrison, C., Turkenburg, J.P., Wilson, K.S.

Revision History

  • 2013-08-07
    Type: Citation | Details: JRNL
  • 2013-07-31
    Type: Entry authorship | Details: AUTHOR
  • 2013-07-31
    Type: Citation | Details: JRNL