3S9W

Crystal structure of Staphylococcal nuclease variant Delta+PHS M98G bound to Ca2+ and thymidine-5',3'-diphosphate at cryogenic temperature

Structural Biology Knowledgebase: 3S9W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3S9W

Classification: HYDROLASE

Total Structure Weight: 16511.74

Macromolecule Entities
Molecule Chains Length Organism Details
Thermonuclease A 143 Staphylococcus aureus EC#: 3.1.31.1 IUBMB
Fragment: Nuclease A (UNP residues 83-231)
Mutation: ΔT126, ΔK127, ΔH128, ΔP129, ΔK130, ΔK131, G50F, V51N, M98G, P117G, H124L, S128A
Gene Name(s): nuc
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A THYMIDINE-3',5'-DIPHOSPHATE
C10 H16 N2 O11 P2
CSNCBOPUCJOHLS-XLPZGREQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.171
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 31.21 α = 90.00
b = 60.53 β = 93.13
c = 38.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-06-02
  • Released Date: 2011-06-22
  • Deposition author(s): Doctrow, B.M., Schlessman, J.L., Garcia-Moreno E., B., Heroux, A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4