4DZD

Crystal structure of the CRISPR-associated protein Cas6e from Escherichia coli str. K-12

• PDB DOI: https://doi.org/10.2210/pdb4DZD/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-01 Released: 2013-03-06 
• Deposition Author(s): Wei, J., Huang, G., Wang, Y., Gong, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Crystal Structure of endoribonuclease Cas6e from Escherichia coli

Wei, J., Huang, G., Wang, Y., Gong, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.45 kDa 
• Atom Count: 1,703 
• Modelled Residue Count: 193 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein ygcH	A	218	Escherichia coli K-12	Mutation(s): 0  Gene Names: ygcH
UniProt
Find proteins for Q46897 (Escherichia coli (strain K12)) Explore Q46897  Go to UniProtKB:  Q46897

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.9	α = 90
b = 59.9	β = 90
c = 128.66	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Wei, J., Huang, G., Wang, Y., Gong, W.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description