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- PDB-6eyy: Anti-CRISPR AcrIIa6 cubic form -

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Basic information

Entry
Database: PDB / ID: 6eyy
TitleAnti-CRISPR AcrIIa6 cubic form
ComponentsAcrIIa6
KeywordsVIRAL PROTEIN / Anti-CRISPR / HTH fold / DNA binding
Function / homology: / Acr-like protein
Function and homology information
Biological speciesStreptococcus phage 73 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCambillau, C. / Amigues, B. / Moineau, S.
CitationJournal: Nat Commun / Year: 2018
Title: Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins.
Authors: Hynes, A.P. / Rousseau, G.M. / Agudelo, D. / Goulet, A. / Amigues, B. / Loehr, J. / Romero, D.A. / Fremaux, C. / Horvath, P. / Doyon, Y. / Cambillau, C. / Moineau, S.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: 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_author.identifier_ORCID
Revision 1.2Aug 14, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AcrIIa6
B: AcrIIa6


Theoretical massNumber of molelcules
Total (without water)42,9292
Polymers42,9292
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-12 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.270, 175.270, 175.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein AcrIIa6


Mass: 21464.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage 73 (virus) / Variant: Steptococcus thermophilus phage D1811 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1S5PRR0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Source detailsStreptococcus thermophilus phage D1176

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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: 5.23 Å3/Da / Density % sol: 76.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride, 0.1M tris pH6.5-7.5, 5-15%(w/v) PEG 8000.
PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32420 / % possible obs: 99.9 % / Redundancy: 26 % / Biso Wilson estimate: 78.08 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.189 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 26 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 32420 / CC1/2: 0.91 / Rrim(I) all: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.84 Å / Cor.coef. Fo:Fc: 0.9288 / Cor.coef. Fo:Fc free: 0.9275 / SU R Cruickshank DPI: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 1620 5 %RANDOM
Rwork0.2316 ---
obs0.2323 32398 99.99 %-
Displacement parametersBiso mean: 64.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.414 Å
Refinement stepCycle: 1 / Resolution: 2.5→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 0 287 3291
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093068HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084120HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1110SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes432HARMONIC5
X-RAY DIFFRACTIONt_it3068HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion21.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion374SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3470SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.58 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3095 148 5.02 %
Rwork0.3139 2798 -
all0.3137 2946 -
obs--99.99 %
Refinement TLS params.

S33: -0.0392 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3060.2702-0.01250.66610.04110.13480.0059-0.058-0.020.03770.03330.04970.0266-0.00160.0101-0.029-0.031-0.11580.01170.068791.4734-20.341449.0635
20.0765-0.0299-0.00840.6893-0.20640.20840.00150.06690.00340.00740.03770.0926-0.0326-0.01170.02070.0312-0.0051-0.0977-0.01470.044288.63010.736836.5997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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