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

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Basic information

Entry
Database: PDB / ID: 4ojp
TitleCrystal Structure of Putative Tailspike Protein (TSP1, orf210) from Escherichia coli O157:H7 Bacteriohage CBA120 in Complex with Maltose
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
alpha-maltose / Tailspike protein
Similarity search - Component
Biological speciesEscherichia phage Cba120 (virus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.948 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 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 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)249,6587
Polymers248,5653
Non-polymers1,0924
Water45,2542512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23420 Å2
ΔGint-125 kcal/mol
Surface area71360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.439, 147.984, 171.038
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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#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.: 2512 / 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: 60.86 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris pH 7.0-7.6, 20% PEG-1000. Soaked with mother liquor containing 37% saturated maltose, VAPOR DIFFUSION, HANGING DROP

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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: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→61.7 Å / Num. all: 228080 / Num. obs: 224635 / % possible obs: 98.5 % / Observed criterion σ(F): 1.47 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 2
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2 / Num. unique all: 16747 / Rsym value: 0.475 / % possible all: 88

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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: 1.948→61.7 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 22.97 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2000 0.89 %random
Rwork0.192 ---
obs0.192 224618 98.54 %-
all-224635 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.948→61.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16990 0 70 2512 19572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817374
X-RAY DIFFRACTIONf_angle_d1.43623629
X-RAY DIFFRACTIONf_dihedral_angle_d12.9936227
X-RAY DIFFRACTIONf_chiral_restr0.0932765
X-RAY DIFFRACTIONf_plane_restr0.0053049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9481-1.99680.38951270.360314154X-RAY DIFFRACTION88
1.9968-2.05080.36411420.315815718X-RAY DIFFRACTION98
2.0508-2.11110.30631420.291115799X-RAY DIFFRACTION99
2.1111-2.17930.281420.267115800X-RAY DIFFRACTION99
2.1793-2.25720.27071410.250615871X-RAY DIFFRACTION99
2.2572-2.34750.27761440.228115897X-RAY DIFFRACTION99
2.3475-2.45440.25991430.215515971X-RAY DIFFRACTION99
2.4544-2.58380.23911440.201815967X-RAY DIFFRACTION99
2.5838-2.74570.23241440.188616059X-RAY DIFFRACTION100
2.7457-2.95770.21171440.178216056X-RAY DIFFRACTION100
2.9577-3.25530.20011450.171516104X-RAY DIFFRACTION100
3.2553-3.72630.17341450.151516189X-RAY DIFFRACTION100
3.7263-4.69450.14291470.131116300X-RAY DIFFRACTION100
4.6945-61.75050.19781500.162716733X-RAY DIFFRACTION100

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