4K6D

Crystal structure of Staphylococcal nuclease variant V23M/T62F at cryogenic temperature

Structural Biology Knowledgebase: 4K6D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4K6D

Classification: HYDROLASE

Total Structure Weight: 17695.19

Macromolecule Entities
Molecule Chains Length Organism Details
Thermonuclease A 149 Staphylococcus aureus EC#: 3.1.31.1 IUBMB
Fragment: Nuclease A (UNP residues 83-231)
Mutation: V23M, T62F
Gene Name(s): nuc

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MPD
Query on MPD

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

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
JSmol
THP
Query on THP

A THYMIDINE-3',5'-DIPHOSPHATE
C10 H16 N2 O11 P2
CSNCBOPUCJOHLS-XLPZGREQSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.190
  • Space Group: P 41
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 47.53 α = 90.00
b = 47.53 β = 90.00
c = 62.75 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-15
  • Released Date: 2013-04-24
  • Deposition author(s): Caro, J.A., Flores, E., Schlessman, J.L., Heroux, A., Garcia-Moreno E., B.

Revision History

No revisions since initial release