[English] 日本語
Yorodumi
- PDB-7mpz: HNH Nuclease Domain from G. stearothermophilus Cas9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mpz
TitleHNH Nuclease Domain from G. stearothermophilus Cas9
ComponentsCRISPR-associated endonuclease Cas9
KeywordsDNA BINDING PROTEIN / nuclease domain / CRISPR Cas9
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, alpha-helical lobe domain / Cas9 alpha-helical lobe domain / RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsD'Ordine, A.M. / Belato, H.B. / Lisi, G.P. / Jogl, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136815 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109035 United States
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Structural and dynamic insights into the HNH nuclease of divergent Cas9 species.
Authors: Belato, H.B. / D'Ordine, A.M. / Nierzwicki, L. / Arantes, P.R. / Jogl, G. / Palermo, G. / Lisi, G.P.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9


Theoretical massNumber of molelcules
Total (without water)18,5081
Polymers18,5081
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.956, 57.956, 119.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 18507.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: cas9, GS458_0313 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A250DVH8, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.12 M [0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol], 0.1 M [MES and imidazole] pH 6.5, 30% (v/v) [40% (v/v) glycerol, 20% (w/v) ...Details: 0.12 M [0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol], 0.1 M [MES and imidazole] pH 6.5, 30% (v/v) [40% (v/v) glycerol, 20% (w/v) polyethylene glycol 4000]

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.04→38.76 Å / Num. obs: 24738 / % possible obs: 99.85 % / Redundancy: 7.3 % / Biso Wilson estimate: 39.68 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 20.31
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 5.6 % / Num. unique obs: 2458 / CC1/2: 0.539 / CC star: 0.837 / % possible all: 99.39

-
Processing

Software
NameVersionClassification
PHENIX1.17rc4_3626refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J9N

6j9n


Resolution: 2.04→38.76 Å / SU ML: 0.2174 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2377 1201 4.86 %
Rwork0.1937 23515 -
obs0.1958 24716 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.48 Å2
Refinement stepCycle: LAST / Resolution: 2.04→38.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 0 67 1229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651184
X-RAY DIFFRACTIONf_angle_d0.81651592
X-RAY DIFFRACTIONf_chiral_restr0.046169
X-RAY DIFFRACTIONf_plane_restr0.0055206
X-RAY DIFFRACTIONf_dihedral_angle_d17.596468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.120.28051180.2612621X-RAY DIFFRACTION99.46
2.12-2.220.3221470.24192593X-RAY DIFFRACTION100
2.22-2.330.27471300.23812629X-RAY DIFFRACTION100
2.34-2.480.32411130.23012644X-RAY DIFFRACTION100
2.48-2.670.24771630.21152570X-RAY DIFFRACTION99.93
2.67-2.940.24251480.20972613X-RAY DIFFRACTION99.82
2.94-3.370.22771120.20722618X-RAY DIFFRACTION99.85
3.37-4.240.23251340.17412607X-RAY DIFFRACTION99.93
4.24-38.760.20451360.16582620X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -16.5146904761 Å / Origin y: -0.401937909455 Å / Origin z: -3.73874303122 Å
111213212223313233
T0.366613125273 Å2-0.0108025064893 Å2-0.0204363618839 Å2-0.323349615826 Å2-0.0655766527862 Å2--0.359753063515 Å2
L1.07076401639 °2-0.317069891484 °2-0.427617817391 °2-1.56411664833 °20.789904441375 °2--2.96858620941 °2
S0.0762601972626 Å °0.235658121297 Å °-0.0776866916242 Å °-0.115074641814 Å °-0.161707442719 Å °0.330738332927 Å °-0.405310235732 Å °-0.227824640769 Å °0.0493831869492 Å °
Refinement TLS groupSelection details: all

+
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