5YJC | pdb_00005yjc

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 (Depositor), 0.216 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 494
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A)) Explore Q5HK94 Go to UniProtKB: Q5HK94
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.216 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

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

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View more in-depth experimental data

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

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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.