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- PDB-5w6s: Crystal structure of Bacteriophage CBA120 tailspike protein 2 enz... -

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Entry
Database: PDB / ID: 5w6s
TitleCrystal structure of Bacteriophage CBA120 tailspike protein 2 enzymatically active domain (TSP2dN, orf211) complex with Escherichia Coli O157-antigen
Componentstailspike protein 2
Keywordsviral protein / hydrolase / Tailspike / CBA120 / O157-antigen
Function / homologymetal ion binding / : / TRIETHYLENE GLYCOL / Putative tail fiber
Function and homology information
Biological speciesEscherichia phage Cba120 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.263 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: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tailspike protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63621
Polymers72,1431
Non-polymers2,49320
Water9,728540
1
A: tailspike protein 2
hetero molecules

A: tailspike protein 2
hetero molecules

A: tailspike protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,90863
Polymers216,4293
Non-polymers7,47960
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area32960 Å2
ΔGint-108 kcal/mol
Surface area57500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.227, 185.227, 185.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-1019-

NA

21A-1020-

K

31A-1101-

HOH

41A-1124-

HOH

51A-1284-

HOH

61A-1398-

HOH

71A-1448-

HOH

81A-1455-

HOH

91A-1509-

HOH

101A-1554-

HOH

111A-1571-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein tailspike protein 2


Mass: 72143.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Cba120 (virus) / Gene: orf211 / Production host: Escherichia coli B (bacteria) / Strain (production host): 384 / References: UniProt: G3M190
#2: Polysaccharide beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-2)-4-acetamido-4,6- ...beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-2)-4-acetamido-4,6-dideoxy-beta-D-mannopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGalpNAca1-2DRhap[4NAc]b1-3LFucpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a1221m-1a_1-5][a1122m-1b_1-5_4*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5]/1-2-3-4/a3-b1_b2-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][a-L-Fucp]{[(3+1)][b-D-Rhap4NAc]{[(2+1)][a-D-GalpNAc]{[(3+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 8 types, 559 molecules

#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 540 / 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: 3.67 Å3/Da / Density % sol: 66.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1M Lithium sulfate, 8% PEG 400, 50mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 94879 / % possible obs: 99 % / Redundancy: 38 % / Net I/σ(I): 26.73

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Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.263→49.504 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.17
RfactorNum. reflection% reflection
Rfree0.1643 4751 5.01 %
Rwork0.1325 --
obs0.1341 94820 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.263→49.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 0 159 540 5752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055300
X-RAY DIFFRACTIONf_angle_d0.7667176
X-RAY DIFFRACTIONf_dihedral_angle_d14.0883056
X-RAY DIFFRACTIONf_chiral_restr0.054822
X-RAY DIFFRACTIONf_plane_restr0.004925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2631-2.28880.2981110.27122150X-RAY DIFFRACTION71
2.2888-2.31570.24981590.22683068X-RAY DIFFRACTION100
2.3157-2.3440.25091560.19843024X-RAY DIFFRACTION100
2.344-2.37360.22081530.19073009X-RAY DIFFRACTION100
2.3736-2.40490.22891630.1713036X-RAY DIFFRACTION100
2.4049-2.43780.1791590.15753029X-RAY DIFFRACTION100
2.4378-2.47260.191630.15323020X-RAY DIFFRACTION100
2.4726-2.50950.16591590.14933049X-RAY DIFFRACTION100
2.5095-2.54870.19091590.15073046X-RAY DIFFRACTION100
2.5487-2.59050.21511630.14393013X-RAY DIFFRACTION100
2.5905-2.63520.16691620.14233031X-RAY DIFFRACTION100
2.6352-2.68310.19281570.13123043X-RAY DIFFRACTION100
2.6831-2.73470.16461640.12712998X-RAY DIFFRACTION100
2.7347-2.79050.15081610.12533052X-RAY DIFFRACTION100
2.7905-2.85120.1761600.12823037X-RAY DIFFRACTION100
2.8512-2.91750.16051590.13512997X-RAY DIFFRACTION100
2.9175-2.99050.1831580.13873032X-RAY DIFFRACTION100
2.9905-3.07130.19411560.14533043X-RAY DIFFRACTION100
3.0713-3.16170.18841620.14683030X-RAY DIFFRACTION100
3.1617-3.26370.17061620.14423048X-RAY DIFFRACTION100
3.2637-3.38030.16971580.13843008X-RAY DIFFRACTION100
3.3803-3.51560.17751610.12913039X-RAY DIFFRACTION100
3.5156-3.67560.13641550.11983023X-RAY DIFFRACTION100
3.6756-3.86930.1121650.11323046X-RAY DIFFRACTION100
3.8693-4.11160.14931550.10873025X-RAY DIFFRACTION100
4.1116-4.42890.141630.09433014X-RAY DIFFRACTION100
4.4289-4.87430.0991650.09213062X-RAY DIFFRACTION100
4.8743-5.57870.14951630.11573012X-RAY DIFFRACTION100
5.5787-7.02540.17581640.14123033X-RAY DIFFRACTION100
7.0254-49.51580.16881560.14513052X-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)
15.38181.34471.13982.83050.49622.44710.05990.8556-0.524-0.25190.1289-0.10040.21580.0959-0.18440.3485-0.0269-0.04180.3664-0.06590.3256-41.3934-53.7165-53.7299
20.39440.19760.23880.43430.33750.83150.0638-0.1702-0.15510.0193-0.0014-0.1819-0.0347-0.0357-0.07640.172-0.0071-0.01170.26530.07020.3239-8.2796-27.3583-4.9285
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 246 through 335 )
2X-RAY DIFFRACTION2chain 'A' and (resid 336 through 921 )

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