5YJC

Structural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm6

PDB DOI: https://doi.org/10.2210/pdb5YJC/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus epidermidis RP62A
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-10-10 Released: 2018-10-17
Deposition Author(s): Zhao, Y.Q., Gu, Y.J., Zhu, X.F., Cheng, W.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.218
R-Value Work: 0.178
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

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

Literature

Structural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm3 and Csm6

Zhao, Y.Q., Gu, Y.J., Zhu, X.F., Cheng, W.

To be published.

Macromolecule Content

Total Structure Weight: 67.52 kDa
Atom Count: 4,538
Modelled Residue Count: 494
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csm6	A, B	284	Staphylococcus epidermidis RP62A	Mutation(s): 0 Gene Names: SERP2456
UniProt
Find proteins for Q5HK94 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A)) Explore Q5HK94 Go to UniProtKB: Q5HK94
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5HK94
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.218
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.141	α = 90
b = 85.399	β = 90
c = 124.898	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
SCALA	data scaling
BUCCANEER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570842

Revision History (Full details and data files)

Version 1.0: 2018-10-17
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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 R01GM133198.