3D4D

Crystal structure of Staphylococcal nuclease variant Delta+PHS Y91E at cryogenic temperature

Structural Biology Knowledgebase: 3D4D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.233

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3D4D

Classification: HYDROLASE

Total Structure Weight: 33103.74

Macromolecule Entities
Molecule Chains Length Organism Details
Thermonuclease A, B 143 Staphylococcus aureus EC#: 3.1.31.1 IUBMB
Mutation: ΔT126, ΔK127, ΔH128, ΔP129, ΔK130, ΔK131, G50F, V51N, Y91E, P117G, H124L, S128A
Gene Name(s): nuc

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.233
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 31.02 α = 90.00
b = 81.29 β = 90.05
c = 60.38 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-05-14
  • Released Date: 2008-11-04
  • Deposition author(s): Khangulov, V.S., Schlessman, J.L., Garcia-Moreno, E.B.

Revision History

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