5XUZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 5XUZ

Classification: HYDROLASE / RNA / DNA

Total Structure Weight: 337581.31


Macromolecule Entities
Molecule Chains Length Organism Details
LbCpf1 A, E 1231 Lachnospiraceae bacterium nd2006
Macromolecule Entities
Molecule Chains Length Organism Details
crRNA B, F 40 Synthetic construct
DNA (29-MER) C, G 29 Synthetic construct
DNA (5'-D(*CP*GP*TP*CP*CP*CP*CP*CP*A)-3') D, H 9 Synthetic construct

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

A, B, E, F 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, E MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B, C, F 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: 2.4 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.177
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 101.95 α = 90.00
b = 103.54 β = 90.00
c = 342.68 γ = 90.00

Structure Validation

View Full Validation Report



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

No revisions since initial release