6M0W | pdb_00006m0w

Crystal structure of Streptococcus thermophilus Cas9 in complex with the AGAA PAM

• PDB DOI: https://doi.org/10.2210/pdb6M0W/pdb
• NAKB: 6M0W

• Classification: HYDROLASE/DNA/RNA
• Organism(s): Streptococcus thermophilus, Streptococcus thermophilus LMD-9
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-02-23 Released: 2020-09-09 
• Deposition Author(s): Zhang, Y., Zhang, H., Xu, X., Wang, Y., Chen, W., Wang, Y., Wu, Z., Tang, N., Wang, Y., Zhao, S., Gan, J., Ji, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.260 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Catalytic-state structure and engineering of Streptococcus thermophilus Cas9

Zhang, Y., Zhang, H., Xu, X., Wang, Y., Chen, W., Wang, Y., Wu, Z., Tang, N., Wang, Y., Zhao, S., Gan, J., Ji, Q.

(2020) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-020-00506-9

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

Macromolecule Content 

• Total Structure Weight: 163.96 kDa 
• Atom Count: 10,518 
• Modeled Residue Count: 1,140 
• Deposited Residue Count: 1,230 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9 1	D [auth A]	1,122	Streptococcus thermophilus LMD-9	Mutation(s): 1  Gene Names: cas9-1, csn1, STER_0709 EC: 3.1
UniProt
Find proteins for Q03LF7 (Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9)) Explore Q03LF7  Go to UniProtKB:  Q03LF7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (72-MER)	A [auth B]	72	Streptococcus thermophilus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	B [auth C]	28	Streptococcus thermophilus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*GP*AP*AP*GP*C)-3')	C [auth D]	8	Streptococcus thermophilus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth B], F [auth D], G [auth A], H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.260 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 321.708	α = 90
b = 75.333	β = 93.47
c = 70.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Zhang, Y., Zhang, H., Xu, X., Wang, Y., Chen, W., Wang, Y., Wu, Z., Tang, N., Wang, Y., Zhao, S., Gan, J., Ji, Q.

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description