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- PDB-6eyx: Anti-CRISPR AcrIIa6 tetragonal form -

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Basic information

Entry
Database: PDB / ID: 6eyx
TitleAnti-CRISPR AcrIIa6 tetragonal form
ComponentsAcrIIa6
KeywordsVIRAL PROTEIN / Anti-CRISPR / HTH fold / DNA binding
Function / homologyAcr-like protein
Function and homology information
Biological speciesStreptococcus phage DT1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 1.2May 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

Downloads & links

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Assembly

Deposited unit
A: AcrIIa6
B: AcrIIa6


Theoretical massNumber of molelcules
Total (without water)43,4132
Polymers43,4132
Non-polymers00
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-12 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.370, 71.370, 177.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein AcrIIa6


Mass: 21706.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage DT1 (virus) / Variant: Streptococcus thermophilus phage D1176. / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9XJC1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
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: 1.96→50 Å / Num. obs: 33785 / % possible obs: 99.5 % / Redundancy: 24 % / Biso Wilson estimate: 37.54 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.139 / Net I/σ(I): 15.8
Reflection shellResolution: 1.96→2.1 Å / Redundancy: 24 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 5971 / CC1/2: 0.88 / Rrim(I) all: 1.17 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→26.38 Å / Cor.coef. Fo:Fc: 0.9338 / Cor.coef. Fo:Fc free: 0.9309 / SU R Cruickshank DPI: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1690 5 %RANDOM
Rwork0.2086 ---
obs0.2095 33785 99.66 %-
Displacement parametersBiso mean: 40.23 Å2
Baniso -1Baniso -2Baniso -3
1--3.1081 Å20 Å20 Å2
2---3.1081 Å20 Å2
3---6.2163 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.96→26.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 0 356 3308
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093014HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014045HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1087SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes424HARMONIC5
X-RAY DIFFRACTIONt_it3014HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion20.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion367SEMIHARMONIC5
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_contact3674SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.02 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.3351 144 5.01 %
Rwork0.2954 2731 -
all0.2974 2875 -
obs--99.66 %
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)
10.30330.24850.25180.9404-0.03991.318-0.01260.07690.025-0.0407-0.0057-0.00880.02140.03640.0184-0.03180.00860.0062-0.07270.00650.001939.43015.20788.4306
20.7681-0.2936-0.17110.16-0.04580.84420.0197-0.0953-0.02920.047-0.00540.00650.0592-0.1134-0.0142-0.0198-0.0376-0.0014-0.01950.0188-0.02129.0583-2.29829.0796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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