3SK8

Crystal structure of Staphylococcal nuclease variant Delta+PHS M98G apo protein at cryogenic temperature

Structural Biology Knowledgebase: 3SK8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.165

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3SK8

Classification: HYDROLASE

Total Structure Weight: 16377.62

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

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

A (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.165
  • Space Group: P 41
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.37 α = 90.00
b = 48.37 β = 90.00
c = 63.45 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-06-22
  • Released Date: 2011-07-06
  • 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