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- PDB-6f7k: Crystal structure of Dettilon tailspike protein (gp208) -

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Basic information

Entry
Database: PDB / ID: 6f7k
TitleCrystal structure of Dettilon tailspike protein (gp208)
ComponentsTailspike
KeywordsSUGAR BINDING PROTEIN / Det7 / dettilon / tailspike / myovirus
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 / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / Tailspike
Function and homology information
Biological speciesSalmonella phage Det7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRoske, Y. / Heinemann, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationBA 4046/1-2 Germany
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Time-resolved DNA release from an O-antigen-specificSalmonellabacteriophage with a contractile tail.
Authors: Broeker, N.K. / Roske, Y. / Valleriani, A. / Stephan, M.S. / Andres, D. / Koetz, J. / Heinemann, U. / Barbirz, S.
History
DepositionDec 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 23, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
B: Tailspike
C: Tailspike
D: Tailspike
F: Tailspike
G: Tailspike
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,31414
Polymers348,4816
Non-polymers5,8338
Water28,6081588
1
A: Tailspike
F: Tailspike
G: Tailspike
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,1797
Polymers174,2413
Non-polymers2,9394
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23400 Å2
ΔGint14 kcal/mol
Surface area47540 Å2
MethodPISA
2
B: Tailspike
C: Tailspike
D: Tailspike
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,1357
Polymers174,2413
Non-polymers2,8954
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23350 Å2
ΔGint10 kcal/mol
Surface area47780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.422, 160.827, 161.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
31G
12B
22C
32D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A252 - 798
2114F252 - 798
3114G252 - 798
1124B252 - 798
2124C252 - 798
3124D252 - 798

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 6 molecules ABCDFG

#1: Protein
Tailspike


Mass: 58080.207 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage Det7 (virus) / Gene: 208, DET7_208 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0C5PVE3

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Sugars , 3 types, 7 molecules

#2: Polysaccharide
alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose-(1-3)-alpha-D- ...alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose-(1-3)-alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 958.860 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-6DManpb1-4LRhapa1-3DGalpa1-6DManpb1-4LRhapa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2211m-1a_1-5][a1122h-1b_1-5][a2112h-1a_1-5]/1-2-3-1-2-3/a4-b1_b6-c1_c3-d1_d4-e1_e6-f1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Galp]{[(3+1)][a-L-Rhap]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Galp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose-(1-3)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 650.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-6DManpb1-4LRhapa1-3DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1a_1-5][a2211m-1a_1-5][a1122h-1b_1-5]/1-2-3-1/a3-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+1)][a-L-Rhap]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Galp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4LRhapa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2211m-1a_1-5][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 1589 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1588 / 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: 2.86 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.85M Succinic acid pH 7.0, 0.1 M HEPES pH 7.0, 1 %(w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→48.76 Å / Num. obs: 231572 / % possible obs: 99.5 % / Redundancy: 6.72 % / Biso Wilson estimate: 45.36 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.0166 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.23 Å / Mean I/σ(I) obs: 0.78 / Num. unique obs: 36799 / CC1/2: 0.452 / Rrim(I) all: 0.2292 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F7D

6f7d


Resolution: 2.1→48.76 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.975 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22068 2432 1.1 %RANDOM
Rwork0.18271 ---
obs0.18312 229138 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.444 Å2
Baniso -1Baniso -2Baniso -3
1--22.31 Å2-0 Å2-0 Å2
2--16.9 Å20 Å2
3---5.42 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24505 0 394 1588 26487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01925474
X-RAY DIFFRACTIONr_bond_other_d0.0010.0222429
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.94734642
X-RAY DIFFRACTIONr_angle_other_deg0.654352137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.67253297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1424.9441068
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.459153793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4351584
X-RAY DIFFRACTIONr_chiral_restr0.0860.24034
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0228756
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025178
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8843.35813140
X-RAY DIFFRACTIONr_mcbond_other2.8843.35813139
X-RAY DIFFRACTIONr_mcangle_it3.7995.03516420
X-RAY DIFFRACTIONr_mcangle_other3.7995.03516421
X-RAY DIFFRACTIONr_scbond_it3.4363.67312334
X-RAY DIFFRACTIONr_scbond_other3.4363.67312335
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7615.40118212
X-RAY DIFFRACTIONr_long_range_B_refined10.72342.1529103
X-RAY DIFFRACTIONr_long_range_B_other10.72342.1529104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A7697medium positional0.360.5
11B7697medium positional0.390.5
11C7697medium positional0.370.5
22A7752medium positional0.360.5
22B7752medium positional0.350.5
22C7752medium positional0.340.5
11A7697medium thermal2.842
11B7697medium thermal3.42
11C7697medium thermal3.42
22A7752medium thermal3.092
22B7752medium thermal3.12
22C7752medium thermal3.242
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 175 -
Rwork0.334 16458 -
obs--97.68 %
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)
10.34450.00990.1760.1818-0.03110.3338-0.0324-0.06290.15910.01810.009-0.0495-0.0301-0.02380.02330.04920.0468-0.01950.06560.00180.1997-20.895740.9031-25.2266
20.1746-0.0182-0.03450.2645-0.20180.51480.00470.08420.0514-0.01520.07820.0668-0.0998-0.3138-0.08290.07930.03380.0260.25440.05360.1066-41.9868-23.2315-60.553
30.3180.1855-0.17550.3677-0.14260.45950.056-0.077-0.01270.125-0.0431-0.1052-0.1358-0.0322-0.0130.1174-0.03420.00130.0810.01670.1147-24.3714-23.2248-39.4345
40.22360.0298-0.14680.2245-0.15330.5225-0.02040.067-0.1195-0.0475-0.0122-0.11240.0889-0.13190.03270.0764-0.06520.03690.0962-0.00370.175-23.133-43.2206-58.3312
50.3265-0.00560.11770.1186-0.04890.32270.0243-0.09090.01090.00220.01960.04750.0966-0.1902-0.04390.083-0.0127-0.02620.1660.04020.1291-40.962622.0288-24.1927
60.3342-0.11270.22210.2516-0.10580.36920.02310.09120.0496-0.1041-0.0021-0.10120.11060.0377-0.0210.11120.02270.00970.08740.03510.1208-22.498221.3645-44.597
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A252 - 798
2X-RAY DIFFRACTION2B252 - 798
3X-RAY DIFFRACTION3C252 - 798
4X-RAY DIFFRACTION4D252 - 798
5X-RAY DIFFRACTION5F252 - 798
6X-RAY DIFFRACTION6G252 - 798

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