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- PDB-8f3k: Anti-CRISPR protein AcrIIC5 inhibits CRISPR-Cas9 by acting as a D... -

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Basic information

Entry
Database: PDB / ID: 8f3k
TitleAnti-CRISPR protein AcrIIC5 inhibits CRISPR-Cas9 by acting as a DNA mimic
ComponentsACRIIC5Nch
KeywordsPROTEIN BINDING / Anti-CRISPR / CRISPR-Cas / Cas9 / inhibition
Function / homologyAMMONIUM ION / Uncharacterized protein
Function and homology information
Biological speciesNeisseria chenwenguii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsShah, M. / Sungwon, H. / Davidson, A.R. / Maxwell, K.L. / Moraes, T.F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06546 Canada
Canadian Institutes of Health Research (CIHR)PJT-180500 Canada
CitationJournal: J.Mol.Biol. / Year: 2023
Title: Anti-CRISPR Protein AcrIIC5 Inhibits CRISPR-Cas9 by Occupying the Target DNA Binding Pocket.
Authors: Hwang, S. / Shah, M. / Garcia, B. / Hashem, N. / Davidson, A.R. / Moraes, T.F. / Maxwell, K.L.
History
DepositionNov 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACRIIC5Nch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,00316
Polymers14,5551
Non-polymers44915
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.622, 46.105, 69.974
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 ACRIIC5Nch


Mass: 14554.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The dataset used is selenium labelled hence Met 87 is labelled as MSE
Source: (gene. exp.) Neisseria chenwenguii (bacteria) / Gene: BG910_04735 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A220S190
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: H4N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5 and 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→38.5 Å / Num. obs: 14852 / % possible obs: 96.77 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.1
Reflection shellResolution: 2.1→38.5 Å / Rmerge(I) obs: 0.0817 / Num. unique obs: 8432 / % possible all: 96.77

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
PHENIX1.20.1-4487phasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.5 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 1492 10.05 %
Rwork0.2045 --
obs0.2097 14852 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 27 59 1042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008933
X-RAY DIFFRACTIONf_angle_d0.7911336
X-RAY DIFFRACTIONf_dihedral_angle_d8.747133
X-RAY DIFFRACTIONf_chiral_restr0.047131
X-RAY DIFFRACTIONf_plane_restr0.008171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.33011430.27981241X-RAY DIFFRACTION99
2.17-2.250.3222960.33551045X-RAY DIFFRACTION80
2.25-2.340.37961340.31131066X-RAY DIFFRACTION85
2.34-2.440.26941380.2441235X-RAY DIFFRACTION99
2.44-2.570.3161530.23811253X-RAY DIFFRACTION99
2.57-2.730.28991370.22661264X-RAY DIFFRACTION98
2.73-2.940.28751250.21651236X-RAY DIFFRACTION96
2.94-3.240.27631430.21171269X-RAY DIFFRACTION100
3.24-3.70.23011370.17621240X-RAY DIFFRACTION98
3.71-4.670.17251440.14551267X-RAY DIFFRACTION99
4.67-38.50.22111420.17561244X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -6.5386 Å / Origin y: 13.1397 Å / Origin z: -9.1798 Å
111213212223313233
T0.1658 Å20.029 Å20.0033 Å2-0.1471 Å2-0.011 Å2--0.1208 Å2
L3.5973 °21.9881 °2-0.8482 °2-3.9778 °2-0.8327 °2--1.9564 °2
S0.0037 Å °-0.0831 Å °0.0073 Å °0.2319 Å °-0.0182 Å °0.1182 Å °-0.0287 Å °-0.151 Å °0.0254 Å °
Refinement TLS groupSelection details: (chain A and resid 11:124)

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