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- PDB-6as4: Structure of a phage anti-CRISPR protein -

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Basic information

Entry
Database: PDB / ID: 6as4
TitleStructure of a phage anti-CRISPR protein
ComponentsNHis AcrE1 anti-crispr protein
KeywordsVIRAL PROTEIN / phage protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPseudomonas phage JBD5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShah, M. / Calmettes, C. / Pawluk, A. / Mejdani, M. / Davidson, A.R. / Maxwell, K.L. / Moraes, T.F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-130482 Canada
Canadian Institutes of Health Research (CIHR)MOP-136845 Canada
CitationJournal: MBio / Year: 2017
Title: Disabling a Type I-E CRISPR-Cas Nuclease with a Bacteriophage-Encoded Anti-CRISPR Protein.
Authors: Pawluk, A. / Shah, M. / Mejdani, M. / Calmettes, C. / Moraes, T.F. / Davidson, A.R. / Maxwell, K.L.
History
DepositionAug 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NHis AcrE1 anti-crispr protein
B: NHis AcrE1 anti-crispr protein
C: NHis AcrE1 anti-crispr protein


Theoretical massNumber of molelcules
Total (without water)36,3653
Polymers36,3653
Non-polymers00
Water2,702150
1
A: NHis AcrE1 anti-crispr protein
B: NHis AcrE1 anti-crispr protein


Theoretical massNumber of molelcules
Total (without water)24,2432
Polymers24,2432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-40 kcal/mol
Surface area10850 Å2
MethodPISA
2
C: NHis AcrE1 anti-crispr protein

C: NHis AcrE1 anti-crispr protein


Theoretical massNumber of molelcules
Total (without water)24,2432
Polymers24,2432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3650 Å2
ΔGint-42 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.740, 63.530, 59.460
Angle α, β, γ (deg.)90.000, 100.340, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NHis AcrE1 anti-crispr protein / phage anti-CRISPR protein


Mass: 12121.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Phage / Source: (gene. exp.) Pseudomonas phage JBD5 (virus) / Gene: JBD5_034 / Plasmid: pET21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L7P7L6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M ammonium citrate dibasic, 20% PEG3350

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→47.585 Å / Num. obs: 23742 / % possible obs: 98.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 37.05 Å2 / Rmerge(I) obs: 0.1033 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.071 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.596 / Mean I/σ(I) obs: 1.57 / CC1/2: 0.529 / % possible all: 97.59

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.22data extraction
XDSdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AcrE1_CHis

Resolution: 2→47.585 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.65
RfactorNum. reflection% reflection
Rfree0.2284 1188 5.01 %
Rwork0.1895 --
obs0.1915 23721 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.89 Å2 / Biso mean: 48.1355 Å2 / Biso min: 22.15 Å2
Refinement stepCycle: final / Resolution: 2→47.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 0 150 2348
Biso mean---45.34 -
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082300
X-RAY DIFFRACTIONf_angle_d0.9283117
X-RAY DIFFRACTIONf_chiral_restr0.038346
X-RAY DIFFRACTIONf_plane_restr0.004415
X-RAY DIFFRACTIONf_dihedral_angle_d14.901868
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 (%)
2-2.0910.34371450.30682741288697
2.091-2.20130.26861470.25462799294698
2.2013-2.33920.25181480.23772795294398
2.3392-2.51980.25631470.2152793294098
2.5198-2.77330.26821490.20642834298399
2.7733-3.17460.23891480.19852822297099
3.1746-3.99930.22511500.16962849299999
3.9993-47.59840.18351540.15742900305499
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)
11.57861.12290.3282.69261.23071.5765-0.12720.26340.05170.02370.10460.22440.0247-0.01360.01190.22210.01330.00190.27190.06260.2541-29.68480.008822.4415
21.51650.6091-0.44962.69041.0752.2179-0.21160.43360.0333-0.36180.4099-0.0967-0.33850.2317-0.18240.2759-0.05740.02270.36880.04410.2711-18.59464.520218.9392
33.5673-0.0261.31363.14530.03792.41390.2212-0.0372-0.36770.17850.0274-0.07820.16280.1312-0.09270.2528-0.0054-0.01380.23420.00310.26745.17271.91823.6064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:96)A3 - 96
2X-RAY DIFFRACTION2(chain B and resid 3:92)B3 - 92
3X-RAY DIFFRACTION3(chain C and resid 2:94)C2 - 94

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