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- PDB-6jhw: Structure of anti-CRISPR AcrIIC3 and NmeCas9 HNH -

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Basic information

Entry
Database: PDB / ID: 6jhw
TitleStructure of anti-CRISPR AcrIIC3 and NmeCas9 HNH
Components
  • AcrIIC3
  • CRISPR-associated endonuclease Cas9
KeywordsPROTEIN BINDING/HYDROLASE / Inhibitor / PROTEIN BINDING / PROTEIN BINDING-HYDROLASE 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 / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas9 / Uncharacterized protein / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSuh, J.Y. / Lee, B.J. / Lee, S.J. / Kim, Y.
CitationJournal: Febs J. / Year: 2019
Title: Anti-CRISPR AcrIIC3 discriminates between Cas9 orthologs via targeting the variable surface of the HNH nuclease domain.
Authors: Kim, Y. / Lee, S.J. / Yoon, H.J. / Kim, N.K. / Lee, B.J. / Suh, J.Y.
History
DepositionFeb 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_entry_details ...entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code ..._entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,0364
Polymers60,0364
Non-polymers00
Water1,31573
1
A: AcrIIC3
B: CRISPR-associated endonuclease Cas9


Theoretical massNumber of molelcules
Total (without water)30,0182
Polymers30,0182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-7 kcal/mol
Surface area13750 Å2
MethodPISA
2
C: AcrIIC3
D: CRISPR-associated endonuclease Cas9


Theoretical massNumber of molelcules
Total (without water)30,0182
Polymers30,0182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-9 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.821, 53.821, 163.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein AcrIIC3


Mass: 13441.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A425B395*PLUS
#2: Protein CRISPR-associated endonuclease Cas9


Mass: 16576.564 Da / Num. of mol.: 2 / Fragment: HNH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: cas9, ERS040961_01379 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0T7L299, UniProt: A1IQ68*PLUS, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence database match UNP A0A3E2QDI5_NEIME was obsoleted with no supersede. There is no match ...The sequence database match UNP A0A3E2QDI5_NEIME was obsoleted with no supersede. There is no match in UniProt.

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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: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.07 M NaCl, 0.05 M sodium citrate, pH 4.5, 22% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 29510 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 36.2
Reflection shellResolution: 2.04→2.08 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1526 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JHV

6jhv


Resolution: 2.04→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.061 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23925 1526 5.2 %RANDOM
Rwork0.21941 ---
obs0.22043 27932 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.219 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å2-0 Å2-0 Å2
2--1.77 Å2-0 Å2
3----3.54 Å2
Refinement stepCycle: 1 / Resolution: 2.04→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 0 73 4271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0144278
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173828
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6635728
X-RAY DIFFRACTIONr_angle_other_deg1.0361.6419016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1535504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41821.429280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41215812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9431544
X-RAY DIFFRACTIONr_chiral_restr0.0750.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024842
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02830
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_it4.5534.3322028
X-RAY DIFFRACTIONr_mcbond_other4.554.332027
X-RAY DIFFRACTIONr_mcangle_it6.4136.4762528
X-RAY DIFFRACTIONr_mcangle_other6.4126.4782529
X-RAY DIFFRACTIONr_scbond_it4.5624.8262250
X-RAY DIFFRACTIONr_scbond_other4.5614.8272251
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4027.0683201
X-RAY DIFFRACTIONr_long_range_B_refined9.1451.1744930
X-RAY DIFFRACTIONr_long_range_B_other9.1451.1824929
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.038→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 94 -
Rwork0.288 2082 -
obs--99.73 %

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