[English] 日本語
Yorodumi
- PDB-6m0w: Crystal structure of Streptococcus thermophilus Cas9 in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m0w
TitleCrystal structure of Streptococcus thermophilus Cas9 in complex with the AGAA PAM
Components
  • CRISPR-associated endonuclease Cas9 1
  • DNA (28-MER)
  • DNA (5'-D(*AP*AP*AP*GP*AP*AP*GP*C)-3')
  • RNA (72-MER)
KeywordsHYDROLASE/DNA/RNA / CRISPR / HYDROLASE-DNA-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
Cas9, PI domain / Cas9, WED domain / CRISPR-Cas9 WED domain / CRISPR-Cas9 PI domain / Cas9, alpha-helical lobe domain / Cas9 alpha-helical lobe domain / RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / HNH endonuclease / CRISPR-associated endonuclease Cas9 ...Cas9, PI domain / Cas9, WED domain / CRISPR-Cas9 WED domain / CRISPR-Cas9 PI domain / Cas9, alpha-helical lobe domain / Cas9 alpha-helical lobe domain / RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9 1
Similarity search - Component
Biological speciesStreptococcus thermophilus LMD-9 (bacteria)
Streptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsZhang, Y. / Zhang, H. / Xu, X. / Wang, Y. / Chen, W. / Wang, Y. / Wu, Z. / Tang, N. / Wang, Y. / Zhao, 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.
CitationJournal: Nat Catal / Year: 2020
Title: Catalytic-state structure and engineering of Streptococcus thermophilus Cas9
Authors: Zhang, Y. / Zhang, H. / Xu, X. / Wang, Y. / Chen, W. / Wang, Y. / Wu, Z. / Tang, N. / Wang, Y. / Zhao, S. / Gan, J. / Ji, Q.
History
DepositionFeb 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: RNA (72-MER)
C: DNA (28-MER)
D: DNA (5'-D(*AP*AP*AP*GP*AP*AP*GP*C)-3')
A: CRISPR-associated endonuclease Cas9 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9619
Polymers163,8404
Non-polymers1225
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22190 Å2
ΔGint-216 kcal/mol
Surface area55250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)321.708, 75.333, 70.300
Angle α, β, γ (deg.)90.000, 93.470, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (28-MER)


Mass: 8496.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus thermophilus (bacteria)
#3: DNA chain DNA (5'-D(*AP*AP*AP*GP*AP*AP*GP*C)-3')


Mass: 2468.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus thermophilus (bacteria)

-
RNA chain / Protein , 2 types, 2 molecules BA

#1: RNA chain RNA (72-MER)


Mass: 23227.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus thermophilus (bacteria)
#4: Protein CRISPR-associated endonuclease Cas9 1 / Cas9**


Mass: 129646.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus LMD-9 (bacteria)
Strain: LMD-9 / Gene: cas9-1, csn1, STER_0709 / Production host: Escherichia coli (E. coli)
References: UniProt: Q03LF7, Hydrolases; Acting on ester bonds

-
Non-polymers , 2 types, 24 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: KCL, MgCL, BaCL2, MBP

-
Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.755→50 Å / Num. obs: 43335 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.19 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Χ2: 0.794 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.76-2.865.60.71240610.7940.3220.7840.73393.7
2.86-2.976.50.58842420.8930.2460.6390.7498.4
2.97-3.116.90.41143510.9580.1680.4440.738100
3.11-3.276.80.25943340.9830.1070.2810.765100
3.27-3.486.50.19943480.9680.0850.2160.786100
3.48-3.756.90.14643690.9920.060.1580.813100
3.75-4.1270.10443720.9910.0420.1120.839100
4.12-4.726.60.0843720.9960.0340.0870.862100
4.72-5.9470.0743930.9970.0280.0760.839100
5.94-506.40.04844930.9980.020.0520.80299.9

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5axw

5axw


Resolution: 2.76→48.874 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.37
RfactorNum. reflection% reflection
Rfree0.2599 2200 5.08 %
Rwork0.2196 --
obs0.2217 43301 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.03 Å2 / Biso mean: 65.2093 Å2 / Biso min: 36.13 Å2
Refinement stepCycle: final / Resolution: 2.76→48.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8247 2247 5 19 10518
Biso mean--79.11 50.66 -
Num. residues----1140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610906
X-RAY DIFFRACTIONf_angle_d0.81715205
X-RAY DIFFRACTIONf_chiral_restr0.0441743
X-RAY DIFFRACTIONf_plane_restr0.0041571
X-RAY DIFFRACTIONf_dihedral_angle_d19.7146310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.76-2.81510.34211270.3464233990
2.8151-2.88050.3651220.3429247497
2.8805-2.95260.35811450.3225253298
2.9526-3.03240.35161490.29472565100
3.0324-3.12160.33891470.27912572100
3.1216-3.22230.29981450.26612559100
3.2223-3.33750.29031390.2472575100
3.3375-3.47110.26661250.24832569100
3.4711-3.6290.28431360.2292580100
3.629-3.82020.26321290.21122617100
3.8202-4.05950.28421260.20082584100
4.0595-4.37270.25371290.19462627100
4.3727-4.81240.23231310.17812592100
4.8124-5.5080.19541640.18672616100
5.508-6.93630.23961480.20342614100
6.9363-48.8740.21561380.19062686100
Refinement TLS params.Method: refined / Origin x: 35.5379 Å / Origin y: 12.3075 Å / Origin z: 146.1941 Å
111213212223313233
T0.4811 Å20.0459 Å20.0237 Å2-0.4398 Å2-0.0374 Å2--0.4994 Å2
L0.9373 °20.1888 °20.4948 °2-0.5444 °2-0.0111 °2--1.3838 °2
S-0.0072 Å °0.0282 Å °-0.0814 Å °-0.0599 Å °0.0542 Å °0.0662 Å °-0.0045 Å °-0.1755 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB-1 - 70
2X-RAY DIFFRACTION1allC1 - 28
3X-RAY DIFFRACTION1allD1 - 8
4X-RAY DIFFRACTION1allA0 - 1121
5X-RAY DIFFRACTION1allE1 - 5
6X-RAY DIFFRACTION1allS1 - 34

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more