5XUS

Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TTTA PAM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 5XUS

Classification: HYDROLASE / RNA / DNA

Total Structure Weight: 168846.48


Macromolecule Entities
Molecule Chains Length Organism Details
LbCpf1 A 1231 Lachnospiraceae bacterium nd2006 Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
crRNA B 40 Synthetic construct
DNA (29-MER) C 29 Synthetic construct
DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*A)-3') D 9 Synthetic construct

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

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-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)
NA
Query on NA

B 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: 2.5 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.178
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 103.21 α = 90.00
b = 103.21 β = 90.00
c = 363.91 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-06-26
  • Released Date: 2017-08-09
  • Deposition author(s): Yamano, T., Nishimasu, H., Ishitani, R., Nureki, O.

Revision History

  • Version 1_0: 2017-08-09

    Type: Initial release

  • Version 1_1: 2017-12-06

    Type: Database references