3NP8

Crystal structure of Staphylococcal nuclease variant Delta+PHS L36A at cryogenic temperature

Structural Biology Knowledgebase: 3NP8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3NP8

Classification: HYDROLASE

Total Structure Weight: 16543.80

Macromolecule Entities
Molecule Chains Length Organism Details
Thermonuclease A 143 Staphylococcus aureus EC#: 3.1.31.1 IUBMB
Fragment: Deletion UNP residues 126-131
Mutation: L36A, ΔT126, ΔK127, ΔH128, ΔP129, ΔK130, ΔK131, G50F, V51N, 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 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: 1.7 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.189
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 31.01 α = 90.00
b = 60.40 β = 93.77
c = 38.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-06-28
  • Released Date: 2011-06-29
  • Deposition author(s): Caro, J.A., Schlessman, J.L., Garcia-Moreno, E.B., Heroux, A.

Revision History

  • 2012-05-23
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4