6M0V | pdb_00006m0v

Crsytal structure of streptococcus thermophilus Cas9 in complex with the GGAA PAM

PDB DOI: https://doi.org/10.2210/pdb6M0V/pdb
NAKB: 6M0V

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

Deposited: 2020-02-22 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.257 (Depositor), 0.250 (DCC)
R-Value Work:
0.213 (Depositor), 0.217 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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

Macromolecule Content

Total Structure Weight: 164.89 kDa
Atom Count: 10,482
Modeled Residue Count: 1,137
Deposited Residue Count: 1,229
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03LF7
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
RNA (71-MER)	A [auth B]	71	Streptococcus thermophilus
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

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

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(APAPGPGPAPAPGPC)-3')	C [auth D]	8	Streptococcus thermophilus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BA Query on BA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	E [auth B] F [auth B] G [auth B] H [auth B] I [auth C] E [auth B], F [auth B], G [auth B], H [auth B], I [auth C], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]