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- PDB-6f7d: Crystal structure of Dettilon tailspike protein (gp208) -

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Basic information

Entry
Database: PDB / ID: 6f7d
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 / Resolution: 1.634 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 8, 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 1.3May 8, 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

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Assembly

Deposited unit
A: Tailspike
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1463
Polymers57,0221
Non-polymers1242
Water8,647480
1
A: Tailspike
hetero molecules

A: Tailspike
hetero molecules

A: Tailspike
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,4399
Polymers171,0663
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Buried area17740 Å2
ΔGint-60 kcal/mol
Surface area46890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.623, 151.623, 151.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-835-

HOH

21A-880-

HOH

31A-965-

HOH

41A-977-

HOH

51A-997-

HOH

61A-1120-

HOH

71A-1175-

HOH

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Components

#1: Protein Tailspike


Mass: 57022.031 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.55 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M 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: 0.91841, 1.009, 1.072
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
21.0091
31.0721
ReflectionResolution: 1.63→47.95 Å / Num. obs: 138026 / % possible obs: 99 % / Redundancy: 3.51 % / Biso Wilson estimate: 25.31 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.0098 / Net I/σ(I): 9.57
Reflection shellResolution: 1.63→1.73 Å / Mean I/σ(I) obs: 1.59 / Num. unique obs: 21954 / CC1/2: 0.639 / Rrim(I) all: 0.0831 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_2579: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 1.634→40.523 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.1877 6894 5 %
Rwork0.1585 --
obs0.16 138012 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.634→40.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 8 480 4501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114132
X-RAY DIFFRACTIONf_angle_d1.1265632
X-RAY DIFFRACTIONf_dihedral_angle_d5.5783210
X-RAY DIFFRACTIONf_chiral_restr0.085644
X-RAY DIFFRACTIONf_plane_restr0.007732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.634-1.65260.33982050.31213944X-RAY DIFFRACTION88
1.6526-1.67210.30612310.27274398X-RAY DIFFRACTION99
1.6721-1.69240.28742290.26314334X-RAY DIFFRACTION100
1.6924-1.71390.30542340.27394430X-RAY DIFFRACTION100
1.7139-1.73640.28742300.29194399X-RAY DIFFRACTION100
1.7364-1.76020.30872320.26844405X-RAY DIFFRACTION100
1.7602-1.78540.27022300.23384453X-RAY DIFFRACTION99
1.7854-1.8120.27372280.22364368X-RAY DIFFRACTION100
1.812-1.84030.22952280.21174332X-RAY DIFFRACTION100
1.8403-1.87050.20892360.19714413X-RAY DIFFRACTION100
1.8705-1.90270.20822410.18344517X-RAY DIFFRACTION100
1.9027-1.93730.18072250.18174267X-RAY DIFFRACTION99
1.9373-1.97460.20262340.17564379X-RAY DIFFRACTION100
1.9746-2.01490.21692280.17894433X-RAY DIFFRACTION100
2.0149-2.05870.21642300.17694386X-RAY DIFFRACTION100
2.0587-2.10660.20832280.16874383X-RAY DIFFRACTION99
2.1066-2.15930.19032320.16214409X-RAY DIFFRACTION100
2.1593-2.21770.20442230.15684353X-RAY DIFFRACTION100
2.2177-2.28290.19672300.15394336X-RAY DIFFRACTION99
2.2829-2.35660.16442350.14874457X-RAY DIFFRACTION100
2.3566-2.44080.21792350.15344393X-RAY DIFFRACTION99
2.4408-2.53850.20912320.15924350X-RAY DIFFRACTION100
2.5385-2.6540.21232350.15274417X-RAY DIFFRACTION99
2.654-2.79390.16582350.1454392X-RAY DIFFRACTION99
2.7939-2.96890.17692240.14624338X-RAY DIFFRACTION99
2.9689-3.19810.15582330.14424349X-RAY DIFFRACTION99
3.1981-3.51970.15152230.13424318X-RAY DIFFRACTION98
3.5197-4.02870.162290.12894371X-RAY DIFFRACTION99
4.0287-5.07410.13912310.10644411X-RAY DIFFRACTION99
5.0741-40.53540.15032280.1494383X-RAY DIFFRACTION99

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