4NCJ

Crystal Structure of Pyrococcus furiosis Rad50 R805E mutation with ADP Beryllium Flouride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.223

Literature

Macromolecules
Sequence Display for 4NCJ

Classification: DNA BINDING PROTEIN

Total Structure Weight: 156392.19

Macromolecule Entities
Molecule Chains Length Organism Details
DNA double-strand break repair Rad50 ATPase A, B, C, D 339 Pyrococcus furiosus Fragment: UNP residues 1-177 and 726-882
Mutation: R805E
Gene Name(s): rad50 PF1167
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BEF
Query on BEF

A, B, C, D BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.223
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 83.02 α = 90.00
b = 108.48 β = 90.00
c = 148.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-24
  • Released Date: 2014-03-05
  • Deposition author(s): Classen, S., Williams, G.J., Arvai, A.S., Williams, R.S.

Revision History

  • Version 1_0: 2014-03-05

    Type: Initial release

  • Version 1_1: 2014-04-02

    Type: Database references

  • Version 1_2: 2017-08-02

    Type: Refinement description, Source and taxonomy