5YJD

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

• PDB DOI: https://doi.org/10.2210/pdb5YJD/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.241 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

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.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.53 kDa 
• Atom Count: 3,043 
• Modelled Residue Count: 368 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csm3	A, B	224	Staphylococcus epidermidis RP62A	Mutation(s): 0  Gene Names: SERP2459
UniProt
Find proteins for Q5HK91 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A)) Explore Q5HK91  Go to UniProtKB:  Q5HK91

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.241 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.623	α = 90
b = 105.76	β = 90
c = 155.977	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Zhao, Y.Q., Gu, Y.J., Zhu, X.F., Cheng, W.

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

Revision History  

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