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- PDB-5w6f: Crystal structure of Bacteriophage CBA120 tailspike protein 3 (TS... -

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Basic information

Entry
Database: PDB / ID: 5w6f
TitleCrystal structure of Bacteriophage CBA120 tailspike protein 3 (TSP3, orf212)
Componentstailspike protein 3
Keywordsviral protein / hydrolase / CBA120 / Tailspike
Function / homologyTail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Right handed beta helix domain / Right handed beta helix region / Periplasmic copper-binding protein (NosD) / Pectin lyase fold / Pectin lyase fold/virulence factor / Tailspike protein
Function and homology information
Biological speciesEscherichia phage Cba120 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.18 Å
AuthorsPlattner, M. / Shneider, M.M. / Leiman, P.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
EPFL0577-1 Switzerland
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120.
Authors: Plattner, M. / Shneider, M.M. / Arbatsky, N.P. / Shashkov, A.S. / Chizhov, A.O. / Nazarov, S. / Prokhorov, N.S. / Taylor, N.M.I. / Buth, S.A. / Gambino, M. / Gencay, Y.E. / Brondsted, L. / ...Authors: Plattner, M. / Shneider, M.M. / Arbatsky, N.P. / Shashkov, A.S. / Chizhov, A.O. / Nazarov, S. / Prokhorov, N.S. / Taylor, N.M.I. / Buth, S.A. / Gambino, M. / Gencay, Y.E. / Brondsted, L. / Kutter, E.M. / Knirel, Y.A. / Leiman, P.G.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tailspike protein 3
B: tailspike protein 3
C: tailspike protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,9574
Polymers206,9213
Non-polymers351
Water22,1401229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27970 Å2
ΔGint-110 kcal/mol
Surface area59680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.580, 66.781, 161.989
Angle α, β, γ (deg.)90.00, 105.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tailspike protein 3


Mass: 68973.828 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Cba120 (virus) / Gene: orf212 / Production host: Escherichia coli B (bacteria) / Strain (production host): 384 / References: UniProt: G3M191
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1229 / 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: 51.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 16% PEG 10000 100mM Tris HCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 205291 / % possible obs: 97 % / Redundancy: 3 % / Net I/σ(I): 6.61

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.18→49.478 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.65
RfactorNum. reflection% reflection
Rfree0.2189 5233 4.96 %
Rwork0.1796 --
obs0.1815 105520 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.18→49.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14100 0 1 1229 15330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314450
X-RAY DIFFRACTIONf_angle_d0.8719636
X-RAY DIFFRACTIONf_dihedral_angle_d11.3895064
X-RAY DIFFRACTIONf_chiral_restr0.0332189
X-RAY DIFFRACTIONf_plane_restr0.0032536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.20470.4394580.38751447X-RAY DIFFRACTION42
2.2047-2.23070.32031700.25993433X-RAY DIFFRACTION99
2.2307-2.25790.26551680.21833319X-RAY DIFFRACTION100
2.2579-2.28650.27921940.21833430X-RAY DIFFRACTION100
2.2865-2.31650.27791650.21323394X-RAY DIFFRACTION100
2.3165-2.34830.24121720.20863367X-RAY DIFFRACTION99
2.3483-2.38180.25931780.19833442X-RAY DIFFRACTION100
2.3818-2.41740.26381780.18523361X-RAY DIFFRACTION99
2.4174-2.45510.23141820.18973405X-RAY DIFFRACTION99
2.4551-2.49540.26591750.1873355X-RAY DIFFRACTION99
2.4954-2.53840.24241620.19793408X-RAY DIFFRACTION99
2.5384-2.58460.25361930.19683392X-RAY DIFFRACTION99
2.5846-2.63430.25931730.18953351X-RAY DIFFRACTION99
2.6343-2.68810.23521800.19183426X-RAY DIFFRACTION99
2.6881-2.74650.21041770.1833359X-RAY DIFFRACTION99
2.7465-2.81040.2321780.18753371X-RAY DIFFRACTION98
2.8104-2.88070.23221790.19443376X-RAY DIFFRACTION99
2.8807-2.95850.26481780.19653415X-RAY DIFFRACTION100
2.9585-3.04560.24711820.20323431X-RAY DIFFRACTION100
3.0456-3.14390.24421790.19713426X-RAY DIFFRACTION100
3.1439-3.25620.24121800.19513420X-RAY DIFFRACTION100
3.2562-3.38660.22711800.19433426X-RAY DIFFRACTION100
3.3866-3.54060.21281810.18243427X-RAY DIFFRACTION99
3.5406-3.72730.191790.18113398X-RAY DIFFRACTION99
3.7273-3.96070.19821770.16383391X-RAY DIFFRACTION99
3.9607-4.26630.19151790.15593382X-RAY DIFFRACTION98
4.2663-4.69540.18431830.1363430X-RAY DIFFRACTION99
4.6954-5.37410.16741820.14453455X-RAY DIFFRACTION99
5.3741-6.76810.19341850.16573517X-RAY DIFFRACTION100
6.7681-49.49040.17881860.15173533X-RAY DIFFRACTION99
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)
13.4115-0.67892.30355.33262.58063.3701-0.291-0.617-0.06080.50340.4802-0.12070.60220.7624-0.18450.52820.09980.05930.91890.01420.324-28.2021-4.230132.7129
20.458-0.4033-1.18920.54840.34715.59130.0338-0.0780.07880.07180.00410.0412-0.6538-0.0104-0.02720.441-0.02160.00740.5626-0.02080.3402-34.14224.16428.6031
30.37290.0378-0.07350.1716-0.12750.98510.0109-0.00150.08460.0288-0.01530.027-0.0984-0.0005-0.00510.22040.0057-0.00640.1861-0.01370.2862-17.981514.5227-65.0886
41.9661-0.00160.45643.1107-1.22371.692-0.1982-0.3181-0.36820.62510.07470.18891.59620.22560.14081.40370.06550.2270.7270.11880.5541-37.4593-28.854224.0257
51.5956-0.01840.2910.96370.40562.8179-0.1042-0.635-0.11740.25650.0725-0.05120.7021.15270.05470.53710.15790.0810.9325-0.00840.3899-21.4072-14.66188.3247
60.66010.3417-0.58130.4527-0.22461.6942-0.0057-0.20080.0490.0056-0.07020.0214-0.07210.3170.0880.2971-0.0123-0.0120.47030.00480.3052-1.94847.1396-36.776
70.6086-0.1295-0.30530.17820.05771.69560.02530.04830.03330.0087-0.0287-0.0417-0.13320.4448-0.00910.2487-0.0677-0.00340.39140.02880.313210.792918.0998-76.9835
84.6147-0.2736-0.46782.52530.08170.8979-0.2133-0.1712-0.14440.3619-0.10840.41540.1455-0.75040.30570.5412-0.09740.19060.9267-0.13340.4644-53.9921-7.119323.7096
93.8242-0.0723-3.10711.36280.86443.8767-0.16490.1942-0.34080.0824-0.40620.04370.7563-0.7240.5530.5276-0.15220.09450.7978-0.09560.3956-46.4757-16.24437.886
100.22350.0103-0.34040.10250.16261.73130.0401-0.1541-0.02150.0728-0.0490.04120.1055-0.02210.0190.2964-0.03020.00130.33670.00570.3185-21.8493-12.4385-37.0481
111.538-1.18341.43161.4793-2.09314.43210.2699-0.0536-0.2588-0.08460.00440.00640.63080.1419-0.31930.26570.0238-0.00280.2384-0.01020.3104-10.1264-11.8138-69.0355
120.4970.1234-0.09870.501-0.47641.37430.00980.1638-0.0327-0.1267-0.0072-0.02070.20510.3370.01370.27660.03940.00130.4032-0.01180.30844.5419-0.4292-85.2025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 178 )
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 627 )
4X-RAY DIFFRACTION4chain 'B' and (resid 12 through 82 )
5X-RAY DIFFRACTION5chain 'B' and (resid 83 through 178 )
6X-RAY DIFFRACTION6chain 'B' and (resid 179 through 397 )
7X-RAY DIFFRACTION7chain 'B' and (resid 398 through 627 )
8X-RAY DIFFRACTION8chain 'C' and (resid 12 through 81 )
9X-RAY DIFFRACTION9chain 'C' and (resid 82 through 125 )
10X-RAY DIFFRACTION10chain 'C' and (resid 126 through 372 )
11X-RAY DIFFRACTION11chain 'C' and (resid 373 through 416 )
12X-RAY DIFFRACTION12chain 'C' and (resid 417 through 627 )

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