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- PDB-5w6h: Crystal structure of Bacteriophage CBA120 tailspike protein 4 enz... -

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Basic information

Entry
Database: PDB / ID: 5w6h
TitleCrystal structure of Bacteriophage CBA120 tailspike protein 4 enzymatically active domain (TSP4dN, orf213)
Componentstailspike protein 4
Keywordsviral protein / hydrolase / Tailspike / CBA120
Function / homologyTail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / ACETATE ION / : / Tailspike protein
Function and homology information
Biological speciesEscherichia virus CBA120
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.289 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 1.1Nov 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 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tailspike protein 4
B: tailspike protein 4
C: tailspike protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,25834
Polymers220,4643
Non-polymers1,79431
Water38,2102121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29540 Å2
ΔGint-120 kcal/mol
Surface area64310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.079, 170.079, 246.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-1574-

HOH

21B-1828-

HOH

31C-1637-

HOH

41C-1872-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein tailspike protein 4


Mass: 73488.062 Da / Num. of mol.: 3 / Mutation: K1012R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus CBA120 / Gene: orf213 / Production host: Escherichia coli B (bacteria) / Strain (production host): 384 / References: UniProt: G3M192

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Non-polymers , 7 types, 2152 molecules

#2: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 2121 / 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: 4.04 Å3/Da / Density % sol: 69.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 3.8 / Details: 700mM Ammonium sulfate 100mM Sodium acetate

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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 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.289→50 Å / Num. obs: 310463 / % possible obs: 99.7 % / Redundancy: 14 % / Net I/σ(I): 18.16

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.289→49.291 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1698 15532 5 %
Rwork0.1397 --
obs0.1412 310372 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.289→49.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15528 0 113 2121 17762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216018
X-RAY DIFFRACTIONf_angle_d0.50621832
X-RAY DIFFRACTIONf_dihedral_angle_d10.5099243
X-RAY DIFFRACTIONf_chiral_restr0.0472566
X-RAY DIFFRACTIONf_plane_restr0.0032839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.289-2.3150.244900.20369274X-RAY DIFFRACTION94
2.315-2.34220.23665190.18329938X-RAY DIFFRACTION100
2.3422-2.37080.21055190.18089782X-RAY DIFFRACTION100
2.3708-2.40080.20385120.17049900X-RAY DIFFRACTION100
2.4008-2.43240.22265260.17549874X-RAY DIFFRACTION100
2.4324-2.46570.21595140.17299821X-RAY DIFFRACTION100
2.4657-2.50090.21685240.17729903X-RAY DIFFRACTION100
2.5009-2.53820.22195210.17049858X-RAY DIFFRACTION100
2.5382-2.57790.20455190.16569787X-RAY DIFFRACTION100
2.5779-2.62020.22475130.16879882X-RAY DIFFRACTION100
2.6202-2.66530.21325090.16619785X-RAY DIFFRACTION99
2.6653-2.71380.20675180.16389806X-RAY DIFFRACTION99
2.7138-2.7660.20775130.16239849X-RAY DIFFRACTION100
2.766-2.82250.19595170.15389844X-RAY DIFFRACTION100
2.8225-2.88380.19135210.15329886X-RAY DIFFRACTION100
2.8838-2.95090.20735250.1579822X-RAY DIFFRACTION100
2.9509-3.02470.19315180.15599880X-RAY DIFFRACTION100
3.0247-3.10640.19015170.15179823X-RAY DIFFRACTION100
3.1064-3.19780.19545180.1449877X-RAY DIFFRACTION100
3.1978-3.3010.16555120.13999786X-RAY DIFFRACTION99
3.301-3.4190.1785200.14359860X-RAY DIFFRACTION100
3.419-3.55580.16635240.14099863X-RAY DIFFRACTION100
3.5558-3.71760.15685240.1329832X-RAY DIFFRACTION100
3.7176-3.91350.13435170.11739885X-RAY DIFFRACTION100
3.9135-4.15860.13985240.10999867X-RAY DIFFRACTION100
4.1586-4.47950.12125140.10479790X-RAY DIFFRACTION100
4.4795-4.92990.11895210.09869841X-RAY DIFFRACTION100
4.9299-5.64240.15035240.11979846X-RAY DIFFRACTION100
5.6424-7.10550.14725160.1369851X-RAY DIFFRACTION100
7.1055-49.30230.15995230.14969828X-RAY DIFFRACTION100
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)
14.1227-0.64653.57260.0345-0.48873.92460.0547-0.0353-0.4263-0.07610.00020.01240.436-0.1297-0.0760.5546-0.0273-0.03820.30980.01250.357212.7798250.9207225.3519
20.1324-0.24180.21720.9047-0.71041.00550.02050.0840.0298-0.1028-0.0788-0.10540.05670.07030.06460.26930.0251-0.00260.23890.02880.275845.6172229.6042270.0223
30.8379-0.05550.14740.8727-0.08150.5994-0.0184-0.024-0.07690.0364-0.0355-0.07280.0966-0.01450.0550.33840.0139-0.02060.23090.01280.291348.2284198.2034308.8715
40.13220.07760.55020.4915-1.25884.71220.06930.0584-0.18330.08060.0862-0.12350.24270.3586-0.16150.29280.0589-0.03370.4359-0.02160.459826.8201266.1849234.5616
50.7519-0.32660.61740.4882-0.72151.2866-0.0776-0.00290.12570.1157-0.0134-0.0938-0.2154-0.07640.10420.360.0327-0.0650.24540.00950.337136.1294251.1154283.6978
60.8073-0.38090.62350.2489-0.21851.0947-0.11980.00750.1460.0499-0.0058-0.1092-0.16110.0870.1360.3281-0.0163-0.10130.27030.02260.385265.6098228.2092314.4007
70.0672-1.13840.7661.9339-1.84750.84870.076-0.03520.0379-0.03390.02670.02890.0793-0.0194-0.10340.4027-0.0158-0.05910.43240.04180.357212.2096252.5335246.9991
80.4642-0.16370.33460.629-0.33471.5128-0.0214-0.0441-0.0421-0.04670.07150.08970.0685-0.2096-0.04240.2307-0.0017-0.04480.24730.020.264322.1334227.1015285.1724
90.4844-0.44730.35030.5243-0.24541.7253-0.1468-0.15710.06460.16490.11460.0168-0.1439-0.2560.02890.32650.0707-0.03070.322-0.0080.284533.1801224.3662324.8509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 433 through 508 )
2X-RAY DIFFRACTION2chain 'A' and (resid 509 through 847 )
3X-RAY DIFFRACTION3chain 'A' and (resid 848 through 1036 )
4X-RAY DIFFRACTION4chain 'B' and (resid 433 through 530 )
5X-RAY DIFFRACTION5chain 'B' and (resid 531 through 811 )
6X-RAY DIFFRACTION6chain 'B' and (resid 812 through 1036 )
7X-RAY DIFFRACTION7chain 'C' and (resid 433 through 599 )
8X-RAY DIFFRACTION8chain 'C' and (resid 600 through 811 )
9X-RAY DIFFRACTION9chain 'C' and (resid 812 through 1036 )

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