4DZD | pdb_00004dzd

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.246 (Depositor), 0.242 (DCC)
R-Value Work:
0.202 (Depositor), 0.206 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of endoribonuclease Cas6e from Escherichia coli

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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 EC: 3.1
UniProt
Find proteins for Q46897 (Escherichia coli (strain K12)) Explore Q46897 Go to UniProtKB: Q46897
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q46897
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.246 (Depositor), 0.242 (DCC)
R-Value Work: 0.202 (Depositor), 0.206 (DCC)
R-Value Observed: 0.204 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.