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- PDB-6j9n: NmeHNH+AcrIIC3 -

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Basic information

Entry
Database: PDB / ID: 6j9n
TitleNmeHNH+AcrIIC3
Components
  • AcrIIC3
  • CRISPR-associated endonuclease Cas9
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AcrIIC3 / HYDROLASE-HYDROLASE INHIBITOR 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
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
: / Uncharacterized protein / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.606 Å
AuthorsZhu, Y.L. / Gao, A. / Serganov, A. / Gao, P.
Funding support United States, China, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM112940 United States
National Science Foundation (China)91753133 China
National Science Foundation (China)31670903 China
CitationJournal: Mol. Cell / Year: 2019
Title: Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type IIC Anti-CRISPR Proteins.
Authors: Zhu, Y. / Gao, A. / Zhan, Q. / Wang, Y. / Feng, H. / Liu, S. / Gao, G. / Serganov, A. / Gao, P.
History
DepositionJan 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9
B: AcrIIC3


Theoretical massNumber of molelcules
Total (without water)33,0112
Polymers33,0112
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-7 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.063, 129.063, 35.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 19388.418 Da / Num. of mol.: 1 / Mutation: E518M,R522M,Q561M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: cas9, NMA510612_0701 / Production host: Escherichia coli (E. coli)
References: UniProt: X5EPV9, Hydrolases; Acting on ester bonds
#2: Protein AcrIIC3


Mass: 13622.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: CIJ84_02095 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E2QDI5, UniProt: A0A425B395*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence of AcrIIC3 was based on protein sequence of published literature (Pawluk et al., PMID: ...Sequence of AcrIIC3 was based on protein sequence of published literature (Pawluk et al., PMID: 27984730), in which reisdues 'MA' at terminal were reported.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M NaCl, 0.1M HEPES, pH 7.5, PEG 400

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 10567 / % possible obs: 99.9 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 26.2
Reflection shellResolution: 2.6→2.66 Å / Rmerge(I) obs: 1.319 / Num. unique obs: 694

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.606→42.246 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.38
RfactorNum. reflection% reflection
Rfree0.2266 569 5.39 %
Rwork0.2051 --
obs0.2063 10556 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.606→42.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 0 4 2211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032249
X-RAY DIFFRACTIONf_angle_d0.643005
X-RAY DIFFRACTIONf_dihedral_angle_d14.746877
X-RAY DIFFRACTIONf_chiral_restr0.045306
X-RAY DIFFRACTIONf_plane_restr0.003393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6065-2.86870.32181210.28932472X-RAY DIFFRACTION100
2.8687-3.28370.31911680.27452434X-RAY DIFFRACTION100
3.2837-4.13650.24091250.19992513X-RAY DIFFRACTION100
4.1365-42.25130.18581550.17862568X-RAY DIFFRACTION100

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