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- PDB-6j9l: FnoBH+AcrIIC2 -

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Basic information

Entry
Database: PDB / ID: 6j9l
TitleFnoBH+AcrIIC2
Components
  • AcrIIC2
  • HNH endonuclease family protein
KeywordsHYDROLASE INHIBITOR/HYDROLASE / AcrIIC2 / HYDROLASE INHIBITOR-HYDROLASE complex
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
CRISPR system subtype II-B RNA-guided endonuclease Cas9/Csx12 / : / CRISPR-associated endonuclease Cas9 alpha-helical lobe / CRISPR-associated endonuclease Cas9, C-terminal domain / Cas9-type HNH domain / Cas9-type HNH domain profile.
Similarity search - Domain/homology
HNH endonuclease family protein / : / Phage associated protein / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Francisella novicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
Revision 1.4Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcrIIC2
B: AcrIIC2
E: HNH endonuclease family protein


Theoretical massNumber of molelcules
Total (without water)34,4213
Polymers34,4213
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-5 kcal/mol
Surface area13630 Å2
Unit cell
Length a, b, c (Å)49.706, 62.525, 88.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AcrIIC2


Mass: 14267.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: CIJ84_02100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E2QCQ3, UniProt: A0A425B3G2*PLUS
#2: Protein/peptide HNH endonuclease family protein


Mass: 5884.802 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella novicida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B6KIH0, UniProt: A0Q5Y3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence of AcrIIC2 was based on protein sequence of published literature (Pawluk et al., PMID: ...Sequence of AcrIIC2 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 Å3/Da / Density % sol: 38.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES, pH 5.6, PEG 3000, PEG 200

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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 PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 27092 / % possible obs: 99.6 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 26.4
Reflection shellResolution: 1.78→1.81 Å / Rmerge(I) obs: 0.398 / Num. unique obs: 1281

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J9K

6j9k


Resolution: 1.78→43.41 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.456 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.249 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22392 1259 4.9 %RANDOM
Rwork0.17725 ---
obs0.1795 24512 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.246 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.78→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 0 211 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192120
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9231.9552857
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8875254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19223.802121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39615381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7471523
X-RAY DIFFRACTIONr_chiral_restr0.0580.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211675
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.80232120
X-RAY DIFFRACTIONr_sphericity_free37.297552
X-RAY DIFFRACTIONr_sphericity_bonded23.59452234
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 69 -
Rwork0.209 1389 -
obs--74.35 %

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