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- PDB-6n05: Structure of anti-crispr protein, AcrIIC2 -

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Basic information

Entry
Database: PDB / ID: 6n05
TitleStructure of anti-crispr protein, AcrIIC2
ComponentsAcrIIC2
KeywordsVIRAL PROTEIN / Prophage protein. Anti-CRISPR
Function / homologyPhage associated protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsShah, M. / Thavalingham, A. / Maxwell, K.L. / Moraes, T.F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-152918 Canada
Canadian Institutes of Health Research (CIHR)FDN-15427 Canada
CitationJournal: Nat Commun / Year: 2019
Title: Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2.
Authors: Thavalingam, A. / Cheng, Z. / Garcia, B. / Huang, X. / Shah, M. / Sun, W. / Wang, M. / Harrington, L. / Hwang, S. / Hidalgo-Reyes, Y. / Sontheimer, E.J. / Doudna, J. / Davidson, A.R. / ...Authors: Thavalingam, A. / Cheng, Z. / Garcia, B. / Huang, X. / Shah, M. / Sun, W. / Wang, M. / Harrington, L. / Hwang, S. / Hidalgo-Reyes, Y. / Sontheimer, E.J. / Doudna, J. / Davidson, A.R. / Moraes, T.F. / Wang, Y. / Maxwell, K.L.
History
DepositionNov 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcrIIC2
B: AcrIIC2


Theoretical massNumber of molelcules
Total (without water)36,4902
Polymers36,4902
Non-polymers00
Water19811
1
A: AcrIIC2
B: AcrIIC2

A: AcrIIC2
B: AcrIIC2


Theoretical massNumber of molelcules
Total (without water)72,9814
Polymers72,9814
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7120 Å2
ΔGint-36 kcal/mol
Surface area22570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.880, 71.880, 135.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein AcrIIC2


Mass: 18245.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: COH52_04850 / Plasmid: pHAT4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A425B3G2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M sodium citrate, 5% propanol and 20% PEG 4000

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9789 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→49.232 Å / Num. obs: 12871 / % possible obs: 99.95 % / Redundancy: 14.1 % / CC1/2: 0.5 / Net I/σ(I): 23.8
Reflection shellResolution: 2.5→2.589 Å / Mean I/σ(I) obs: 1.45 / Num. unique obs: 1250 / CC1/2: 0.684 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIXphasing
Cootmodel building
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→49.232 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.54
RfactorNum. reflection% reflection
Rfree0.2467 1169 5.01 %
Rwork0.2119 --
obs0.2137 12868 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 251 Å2 / Biso min: 39.81 Å2
Refinement stepCycle: final / Resolution: 2.5→49.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 0 11 1754
Biso mean---65.45 -
Num. residues----215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.61380.34831430.342127522895100
2.6138-2.75160.38881410.320728032944100
2.7516-2.9240.30191440.273627662910100
2.924-3.14970.30961480.255927912939100
3.1497-3.46660.26571520.216527542906100
3.4666-3.9680.21261450.19227862931100
3.968-4.99850.20841460.169827882934100
4.9985-49.24190.24141500.20722723287398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.3986-0.388-1.6055.25140.52688.4389-0.3133-0.66840.02130.1020.16870.32290.1699-0.17540.070.56650.0188-0.03360.34960.04230.43945.86141.532753.3952
28.10930.5446-1.84147.1923-0.0554.5593-0.3863-0.5362-0.0826-0.010.2381-0.68950.60240.81490.16150.64550.1690.00310.6110.04340.380428.187338.839446.589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:112)A6 - 112
2X-RAY DIFFRACTION2(chain B and resid 6:111)B6 - 111

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