3EJI

Crystal structure of Staphylococcal nuclease variant Delta+PHS L36K at cryogenic temperature

Structural Biology Knowledgebase: 3EJI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.203

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EJI

Classification: HYDROLASE

Total Structure Weight: 16372.78

Macromolecule Entities
Molecule Chains Length Organism Details
Thermonuclease A 143 Staphylococcus aureus EC#: 3.1.31.1 IUBMB
Fragment: UNP residues 80-228
Mutation: L36K, ΔT123, ΔK124, ΔH125, ΔP126, ΔK127, ΔK128, G50F, V51N, P117G, 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
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: 0.272
  • R-Value Work: 0.203
  • Space Group: P 41
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.20 α = 90.00
b = 48.20 β = 90.00
c = 63.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-18
  • Released Date: 2008-11-04
  • Deposition author(s): Khangulov, V.S., Schlessman, J.L., Garcia-Moreno, E.B., Benning, M., Isom, D.

Revision History

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