5B2R

Crystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex with sgRNA and target DNA (TGA PAM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 5B2R

Classification: HYDROLASE / RNA / DNA

Total Structure Weight: 196931.13


Macromolecule Entities
Molecule Chains Length Organism Details
CRISPR-associated endonuclease Cas9 B 1372 Streptococcus pyogenes EC#: 3.1 IUBMB
Mutation: D10A, C80L, C574E, H840A, D1135V, R1335Q, T1337R
Gene Name(s): cas9 csn1 SPy_1046
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
Guide RNA A 81 Streptococcus pyogenes
Target DNA C 28 Streptococcus pyogenes
Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3') D 8 Streptococcus pyogenes

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

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B 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: 0.230
  • R-Value Work: 0.200
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 177.76 α = 90.00
b = 67.74 β = 111.23
c = 187.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-02-02
  • Released Date: 2016-03-23
  • Deposition author(s): Hirano, S., Nishimasu, H., Ishitani, R., Nureki, O.

Revision History

  • 2016-04-06
    Type: Database references