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- PDB-6jhv: Structure of anti-CRISPR AcrIIC3 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6jhv
TitleStructure of anti-CRISPR AcrIIC3
ComponentsAcrIIC3
KeywordsPROTEIN BINDING / Inhibitor
Function / homologyUncharacterized protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.321 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_db_accession / _struct_ref.pdbx_seq_one_letter_code / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcrIIC3
B: AcrIIC3


Theoretical massNumber of molelcules
Total (without water)27,2842
Polymers27,2842
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-0 kcal/mol
Surface area12840 Å2
Unit cell
Length a, b, c (Å)74.208, 47.919, 71.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein AcrIIC3


Mass: 13642.178 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.38 Å3/Da / Density % sol: 48.43 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20 mM HEPES-NaOH, pH 7.4, 200 mM NaCl, 5% (v/v) glycerol, 2 mM BME

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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 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 11533 / % possible obs: 99.7 % / Redundancy: 17.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 38.8
Reflection shellResolution: 2.32→2.36 Å / Rmerge(I) obs: 0.429 / Num. unique obs: 553

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.321→35.707 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.88
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2415 2140 10.09 %
Rwork0.1904 --
obs0.1956 11533 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.321→35.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 0 114 1990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081908
X-RAY DIFFRACTIONf_angle_d0.8642560
X-RAY DIFFRACTIONf_dihedral_angle_d3.1041164
X-RAY DIFFRACTIONf_chiral_restr0.046280
X-RAY DIFFRACTIONf_plane_restr0.004330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3209-2.37480.28311480.23261235X-RAY DIFFRACTION98
2.3748-2.43420.34051470.23011264X-RAY DIFFRACTION100
2.4342-2.50.2551500.21161269X-RAY DIFFRACTION100
2.5-2.57350.26521380.21991286X-RAY DIFFRACTION100
2.5735-2.65660.27591430.20971293X-RAY DIFFRACTION100
2.6566-2.75150.25751480.22271254X-RAY DIFFRACTION100
2.7515-2.86160.2711350.22931303X-RAY DIFFRACTION100
2.8616-2.99180.23361340.21081282X-RAY DIFFRACTION100
2.9918-3.14940.29641350.20381271X-RAY DIFFRACTION100
3.1494-3.34660.28541390.20031282X-RAY DIFFRACTION100
3.3466-3.60480.25631440.19291256X-RAY DIFFRACTION100
3.6048-3.96720.21741430.15881296X-RAY DIFFRACTION100
3.9672-4.54020.2051480.15511261X-RAY DIFFRACTION100
4.5402-5.71640.20231460.16831274X-RAY DIFFRACTION100
5.7164-35.71120.19231420.17671243X-RAY DIFFRACTION98

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