5XH6

Crystal structure of the Acidaminococcus sp. BV3L6 Cpf1 RVR variant in complex with crRNA and target DNA (TATA PAM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.175

Literature

Macromolecules
Sequence Display for 5XH6

Classification: HYDROLASE / RNA / DNA

Total Structure Weight: 180246.86


Macromolecule Entities
Molecule Chains Length Organism Details
CRISPR-associated endonuclease Cpf1 A 1310 Acidaminococcus sp. bv3l6 EC#: 3.1 IUBMB
Mutation: S542R, K548V, N552R
Gene Name(s): cpf1 HMPREF1246_0236
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
crRNA B 43 Acidaminococcus sp. bv3l6 RNA (40-MER)
Target DNA strand C 34 Acidaminococcus sp. bv3l6 DNA (30-MER)
Non-target DNA strand D 10 Acidaminococcus sp. bv3l6 DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*AP*TP*A)-3')

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

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

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, C SODIUM ION
Na
FKNQFGJONOIPTF-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: 0.210
  • R-Value Work: 0.175
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 81.16 α = 90.00
b = 133.68 β = 90.00
c = 199.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-04-19
  • Released Date: 2017-06-14
  • Deposition author(s): Nishimasu, H., Yamano, T., Ishitani, R., Nureki, O.

Revision History

  • Version 1_0: 2017-06-14

    Type: Initial release

  • Version 1_1: 2017-07-26

    Type: Database references