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- PDB-6as3: Structure of a phage anti-CRISPR protein -

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Basic information

Entry
Database: PDB / ID: 6as3
TitleStructure of a phage anti-CRISPR protein
ComponentsNHis AcrE1 protein
KeywordsUNKNOWN FUNCTION / 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 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: NHis AcrE1 protein
B: NHis AcrE1 protein
C: NHis AcrE1 protein
D: NHis AcrE1 protein


Theoretical massNumber of molelcules
Total (without water)48,5864
Polymers48,5864
Non-polymers00
Water7,782432
1
A: NHis AcrE1 protein
C: NHis AcrE1 protein


Theoretical massNumber of molelcules
Total (without water)24,2932
Polymers24,2932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-41 kcal/mol
Surface area10850 Å2
MethodPISA
2
B: NHis AcrE1 protein
D: NHis AcrE1 protein


Theoretical massNumber of molelcules
Total (without water)24,2932
Polymers24,2932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-42 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.799, 87.462, 91.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NHis AcrE1 protein


Mass: 12146.588 Da / Num. of mol.: 4 / Mutation: H86Y
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.: 432 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Tris pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→63.09 Å / Num. obs: 34051 / % possible obs: 99.99 % / Redundancy: 9.2 % / Biso Wilson estimate: 22.73 Å2 / Net I/σ(I): 18.91
Reflection shellResolution: 2→2.071 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 3.97 / Num. unique obs: 3351 / CC1/2: 0.703 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.22data extraction
XDSdata processing
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ARZ

6arz


Resolution: 2→63.09 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.82
RfactorNum. reflection% reflection
Rfree0.2141 1742 5.12 %
Rwork0.164 --
obs0.1666 34044 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.95 Å2 / Biso mean: 31.9875 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 2→63.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 0 432 3386
Biso mean---39.03 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073126
X-RAY DIFFRACTIONf_angle_d0.8774261
X-RAY DIFFRACTIONf_chiral_restr0.038482
X-RAY DIFFRACTIONf_plane_restr0.004561
X-RAY DIFFRACTIONf_dihedral_angle_d15.071206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.05890.26421440.208626452789
2.0589-2.12530.22661430.18726402783
2.1253-2.20130.2161550.167326552810
2.2013-2.28940.21651260.163326712797
2.2894-2.39360.23171340.164426612795
2.3936-2.51980.21871560.157826552811
2.5198-2.67770.191390.163926882827
2.6777-2.88440.22911470.179126592806
2.8844-3.17470.24671590.171626802839
3.1747-3.63410.20991210.157327522873
3.6341-4.57830.19621630.143227342897
4.5783-63.1240.19551550.165628623017
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)
12.2474-0.9289-0.21162.5771-0.04511.09960.1039-0.08730.05960.17890.00320.1363-0.0893-0.0362-0.08880.1443-0.03910.03120.1483-0.00590.153619.0164-15.0716-1.1196
22.0668-1.7780.77352.3924-0.84970.71020.0147-0.1342-0.06510.07140.04490.01-0.0114-0.0791-0.0670.1532-0.02790.01360.18780.02070.189535.469614.82330.2912
31.8833-0.74220.03632.4810.13491.53010.17830.2046-0.0521-0.1233-0.04550.0537-0.02340.058-0.15530.13550.00150.00850.19570.00730.1223.0532-13.2918-12.3618
42.2072-0.54290.50721.695-0.46861.05980.28210.0841-0.3556-0.166-0.0685-0.01890.1803-0.0132-0.14460.18360.0002-0.03390.187-0.00940.197831.131511.1657-10.4377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:96)A2 - 96
2X-RAY DIFFRACTION2(chain B and resid 2:95)B2 - 95
3X-RAY DIFFRACTION3(chain C and resid 2:92)C2 - 92
4X-RAY DIFFRACTION4(chain D and resid 3:92)D3 - 92

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