7VK9 | pdb_00007vk9

Crystal structure of xCas9 P411T

• PDB DOI: https://doi.org/10.2210/pdb7VK9/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Streptococcus pyogenes serotype M1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-09-29 Released: 2022-04-06 
• Deposition Author(s): Bao, R., Liu, H.Y., Luo, Y.Z., Song, Y.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structural and Dynamics Studies of the Spcas9 Variant Provide Insights into the Regulatory Role of the REC1 Domain

Liu, H., Zhou, Y., Song, Y., Zhang, Q., Kan, Y., Tang, X., Xiao, Q., Xiang, Q., Liu, H., Luo, Y., Bao, R.

(2022) ACS Catal 12: 8687-8697

• DOI: https://doi.org/10.1021/acscatal.2c01804

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 158.65 kDa 
• Atom Count: 10,529 
• Modeled Residue Count: 1,279 
• Deposited Residue Count: 1,368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9/Csn1	A	1,368	Streptococcus pyogenes serotype M1	Mutation(s): 8  Gene Names: cas9, csn1, SPy_1046 EC: 3.1
UniProt
Find proteins for Q99ZW2 (Streptococcus pyogenes serotype M1) Explore Q99ZW2  Go to UniProtKB:  Q99ZW2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.023	α = 90
b = 190.023	β = 90
c = 142.985	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Bao, R., Liu, H.Y., Luo, Y.Z., Song, Y.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81670008

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2022-10-19
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description