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

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Basic information

Entry
Database: PDB / ID: 4ojl
TitleCrystal Structure of Putative Tailspike Protein (TSP1, orf210) from Escherichia coli O157:H7 Bacteriohage CBA120 in Complex with Glucose
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
beta-D-glucopyranose / Tailspike protein
Similarity search - Component
Biological speciesEscherichia phage Cba120 (virus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 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 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)249,3518
Polymers248,5653
Non-polymers7865
Water44,4432467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22750 Å2
ΔGint-114 kcal/mol
Surface area72240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.448, 152.442, 171.852
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: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 2467 / 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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris pH 7.0-7.6, 20% PEG-1000. Soaked in 37% saturated glucose mother liquor, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→43.8 Å / Num. all: 218091 / Num. obs: 209831 / % possible obs: 96.2 % / Observed criterion σ(F): 1.49 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 13
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.9 / Num. unique all: 14729 / Rsym value: 0.439 / % possible all: 92.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: SeMet Tailspike structure

Resolution: 2→43.8 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 19.77 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 10566 5.04 %Random
Rwork0.1781 ---
obs0.1798 209800 96.21 %-
all-218091 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17005 0 49 2467 19521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717365
X-RAY DIFFRACTIONf_angle_d1.42723611
X-RAY DIFFRACTIONf_dihedral_angle_d13.0796225
X-RAY DIFFRACTIONf_chiral_restr0.0912756
X-RAY DIFFRACTIONf_plane_restr0.0063052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.31893470.29786178X-RAY DIFFRACTION91
2.0227-2.04650.30963080.28126380X-RAY DIFFRACTION93
2.0465-2.07150.30253360.26446462X-RAY DIFFRACTION94
2.0715-2.09770.27233290.25886416X-RAY DIFFRACTION94
2.0977-2.12530.29883570.25856403X-RAY DIFFRACTION94
2.1253-2.15440.29573690.24916458X-RAY DIFFRACTION94
2.1544-2.18520.30343520.24266473X-RAY DIFFRACTION95
2.1852-2.21780.26163650.23366467X-RAY DIFFRACTION95
2.2178-2.25250.25863450.22196542X-RAY DIFFRACTION95
2.2525-2.28940.25562980.21316568X-RAY DIFFRACTION95
2.2894-2.32890.23293890.2066537X-RAY DIFFRACTION96
2.3289-2.37120.23023140.20056566X-RAY DIFFRACTION96
2.3712-2.41680.23333590.19366582X-RAY DIFFRACTION96
2.4168-2.46620.23333740.19126550X-RAY DIFFRACTION96
2.4662-2.51980.24243270.19466660X-RAY DIFFRACTION96
2.5198-2.57840.2173430.18976610X-RAY DIFFRACTION96
2.5784-2.64290.23523560.18366631X-RAY DIFFRACTION97
2.6429-2.71430.22733460.18146665X-RAY DIFFRACTION97
2.7143-2.79420.21163460.1776695X-RAY DIFFRACTION97
2.7942-2.88430.21143490.1776706X-RAY DIFFRACTION97
2.8843-2.98740.21713610.1756704X-RAY DIFFRACTION97
2.9874-3.1070.18893840.17116735X-RAY DIFFRACTION98
3.107-3.24840.21133630.17236770X-RAY DIFFRACTION98
3.2484-3.41960.20163880.16366773X-RAY DIFFRACTION98
3.4196-3.63370.19283490.15426830X-RAY DIFFRACTION98
3.6337-3.91420.17213660.14156819X-RAY DIFFRACTION98
3.9142-4.30780.1573680.13056870X-RAY DIFFRACTION99
4.3078-4.93050.13883650.11286946X-RAY DIFFRACTION99
4.9305-6.20950.16033480.14127038X-RAY DIFFRACTION99
6.2095-45.80510.18333650.16647200X-RAY DIFFRACTION98

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