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- PDB-4oj5: Crystal Structure of a Putative Tailspike Protein (TSP1, orf210) ... -

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Basic information

Entry
Database: PDB / ID: 4oj5
TitleCrystal Structure of a Putative Tailspike Protein (TSP1, orf210) from Escherichia coli O157:H7 Bacteriohage CBA120
ComponentsTailspike protein
KeywordsVIRAL PROTEIN / parallel beta helix / putative endo-glycosidase / bacterial polysaccharide / phage baseplate / phage tail
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component / metal ion binding
Similarity search - Function
Pectate Lyase C-like - #130 / Seminal Fluid Protein PDC-109 (Domain B) - #80 / NE0471 N-terminal domain-like - #50 / NE0471 N-terminal domain-like / Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Seminal Fluid Protein PDC-109 (Domain B) / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold ...Pectate Lyase C-like - #130 / Seminal Fluid Protein PDC-109 (Domain B) - #80 / NE0471 N-terminal domain-like - #50 / NE0471 N-terminal domain-like / Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Seminal Fluid Protein PDC-109 (Domain B) / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / 3 Solenoid / Ribbon / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia phage Cba120 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsChen, C. / Herzberg, O.
CitationJournal: Plos One / Year: 2014
Title: Crystal structure of ORF210 from E. coli O157:H1 phage CBA120 (TSP1), a putative tailspike protein.
Authors: Chen, C. / Bales, P. / Greenfield, J. / Heselpoth, R.D. / Nelson, D.C. / Herzberg, O.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tailspike protein
B: Tailspike protein
C: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,6314
Polymers248,5653
Non-polymers651
Water44,1192449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21690 Å2
ΔGint-122 kcal/mol
Surface area71530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.621, 147.823, 170.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tailspike protein


Mass: 82855.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Cba120 (virus) / Gene: orf210 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G3M189
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2449 / 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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris pH 7.0-7.6, 20% PEG-1000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2012 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→73.9 Å / Num. all: 287650 / Num. obs: 287155 / % possible obs: 99.8 % / Observed criterion σ(F): 1.45 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / Num. unique all: 20996 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: SeMet Tailspike protein structure

Resolution: 1.8→63.438 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 23.02 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 14894 5 %random
Rwork0.1866 ---
obs0.1867 287138 99.83 %-
all-287650 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→63.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16972 0 1 2449 19422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717284
X-RAY DIFFRACTIONf_angle_d1.42323502
X-RAY DIFFRACTIONf_dihedral_angle_d12.8826176
X-RAY DIFFRACTIONf_chiral_restr0.0922735
X-RAY DIFFRACTIONf_plane_restr0.0053045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.39641400.37420083X-RAY DIFFRACTION100
1.845-1.89490.33251430.336320222X-RAY DIFFRACTION100
1.8949-1.95070.34321410.305720204X-RAY DIFFRACTION100
1.9507-2.01360.32171420.278520147X-RAY DIFFRACTION100
2.0136-2.08560.24061420.248920287X-RAY DIFFRACTION100
2.0856-2.16910.23881420.225920236X-RAY DIFFRACTION100
2.1691-2.26780.22971420.205920289X-RAY DIFFRACTION100
2.2678-2.38740.21641430.190620315X-RAY DIFFRACTION100
2.3874-2.5370.17841420.184420312X-RAY DIFFRACTION100
2.537-2.73290.20191430.179220369X-RAY DIFFRACTION100
2.7329-3.00790.19331430.176820422X-RAY DIFFRACTION100
3.0079-3.44310.18671440.162920502X-RAY DIFFRACTION100
3.4431-4.33780.15951440.134120622X-RAY DIFFRACTION100
4.3378-63.4770.15261490.143821128X-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)
10.46110.3589-0.30450.3521-0.30.3236-0.12780.1713-0.0336-0.1120.1024-0.03020.127-0.0997-0.00470.1723-0.04930.01250.1408-0.03170.107451.878201.746412.895
20.43770.3114-0.54030.2165-0.4030.73990.0520.10240.12720.01780.09150.0783-0.0236-0.09890.10250.08080.01870.0290.12130.03980.131742.2423220.99920.178
30.23830.2671-0.28960.3155-0.39060.45270.0113-0.0367-0.00510.0082-0.03050.0027-0.00670.06690.00750.1024-0.00510.00570.0478-0.00660.084760.840621330.4241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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