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

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Basic information

Entry
Database: PDB / ID: 6arz
TitleStructure of a phage anti-CRISPR protein
ComponentsUncharacterized protein
KeywordsVIRAL PROTEIN / Prophage protein. Anti-CRISPR
Function / homologyBROMIDE ION / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas phage JBD5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsCalmettes, C. / Shah, M. / Pawluk, A. / Davidson, A.R. / Maxwell, K.L. / Moraes, T.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canada
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Structure and function of a type I-E anti-CRISPR protein
Authors: Pawluk, A. / Shah, M. / Calmettes, C. / Mejdani, M. / 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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,15111
Polymers37,3733
Non-polymers7788
Water1,892105
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6139
Polymers24,9152
Non-polymers6987
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-41 kcal/mol
Surface area10550 Å2
MethodPISA
2
C: Uncharacterized protein
hetero molecules

C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0754
Polymers24,9152
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3900 Å2
ΔGint-44 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.137, 63.959, 59.701
Angle α, β, γ (deg.)90.000, 100.940, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPchain AAA1 - 961 - 96
2GLYGLYchain BBB1 - 921 - 92
3ALAALAchain CCC1 - 941 - 94

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Components

#1: Protein Uncharacterized protein / phage anti-CRISPR protein


Mass: 12457.624 Da / Num. of mol.: 3 / Fragment: AcrE1
Source method: isolated from a genetically manipulated source
Details: Phage / Source: (gene. exp.) Pseudomonas phage JBD5 (virus) / Gene: JBD5_034 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L7P7L6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1M sodium cacodylate pH 6.1, 23% PEG 3350, 0.5M sodium bromide, and 7% glycerol

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.919 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.5→48.177 Å / Num. obs: 24655 / % possible obs: 99.94 % / Redundancy: 7.7 % / Biso Wilson estimate: 45.82 Å2 / Net I/σ(I): 24.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→48.177 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.43
RfactorNum. reflection% reflection
Rfree0.2208 1232 5 %
Rwork0.1795 --
obs0.1815 24650 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 275.51 Å2 / Biso mean: 58.8522 Å2 / Biso min: 24.84 Å2
Refinement stepCycle: final / Resolution: 2.5→48.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 30 105 2358
Biso mean--71.9 52.27 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122272
X-RAY DIFFRACTIONf_angle_d1.293055
X-RAY DIFFRACTIONf_chiral_restr0.061337
X-RAY DIFFRACTIONf_plane_restr0.006399
X-RAY DIFFRACTIONf_dihedral_angle_d16.415856
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1272X-RAY DIFFRACTION9.797TORSIONAL
12B1272X-RAY DIFFRACTION9.797TORSIONAL
13C1272X-RAY DIFFRACTION9.797TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.60010.31971350.243825842719
2.6001-2.71840.31451370.222526262763
2.7184-2.86170.25381400.230225662706
2.8617-3.0410.27941390.21926142753
3.041-3.27580.24791390.211826242763
3.2758-3.60530.25171340.182425852719
3.6053-4.12680.22971350.16726082743
4.1268-5.19830.17511370.14726022739
5.1983-48.18570.16761360.156426092745
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)
18.9665-0.3235-2.17729.16926.13525.1662-0.78670.75640.068-0.3530.64350.22480.67480.02390.19560.7219-0.21460.01330.66320.0810.360819.978124.23067.1618
20.98570.4916-0.58014.64184.27266.5232-0.0947-0.08520.25980.24040.00570.33190.0436-0.1690.11380.32820.04790.01080.33010.06650.388820.992241.054629.9616
36.76861.63090.03832.7889-2.14593.0316-0.27180.60240.49681.07590.38340.50260.5036-0.7048-0.14040.5048-0.08260.05050.4699-0.0030.50599.595229.265525.4853
45.3773.1150.43844.62474.1345.5178-0.84551.53910.2686-1.24290.56740.0686-0.29860.13580.20860.7702-0.27370.03650.92310.11210.447627.385329.19133.2615
50.87731.15871.5444.07354.73847.2757-0.1790.1180.0523-0.13190.33710.0027-0.58590.5996-0.17370.3822-0.02620.00330.42840.04960.404630.150941.549528.5738
69.95325.8852-1.96363.8562-2.56376.6462-0.1905-0.20210.8643-1.6210.7615-0.8593-1.59530.9386-0.41350.9346-0.39050.23160.8061-0.14560.630239.160442.479614.1798
77.56970.14711.57949.2498-0.86145.3492-0.1538-0.06241.26780.6449-0.02010.3998-1.0022-0.03440.06380.5823-0.05860.00240.318-0.04560.451250.512350.75264.3979
84.92940.5644-0.98776.1201-1.13494.75610.34310.1506-1.7314-0.3318-0.1752-0.24351.08220.0756-0.03860.72520.0391-0.16960.4069-0.01960.782854.053119.85870.6757
94.04572.4352.10686.98484.33229.01520.2252-0.0089-0.10240.32920.1515-0.92761.05710.3332-0.28410.36630.0248-0.07230.3392-0.01930.405960.89535.6817.4531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:29)A1 - 29
2X-RAY DIFFRACTION2(chain A and resid 30:80)A30 - 80
3X-RAY DIFFRACTION3(chain A and resid 81:96)A81 - 96
4X-RAY DIFFRACTION4(chain B and resid 1:28)B1 - 28
5X-RAY DIFFRACTION5(chain B and resid 29:80)B29 - 80
6X-RAY DIFFRACTION6(chain B and resid 81:92)B81 - 92
7X-RAY DIFFRACTION7(chain C and resid 2:38)C2 - 38
8X-RAY DIFFRACTION8(chain C and resid 39:74)C39 - 74
9X-RAY DIFFRACTION9(chain C and resid 75:94)C75 - 94

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