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- PDB-7rfv: Tailspike protein 4 (TSP4) from phage CBA120, residues 1-250, obt... -

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Basic information

Entry
Database: PDB / ID: 7rfv
TitleTailspike protein 4 (TSP4) from phage CBA120, residues 1-250, obtained in the presence of PEG8000
ComponentsTailspike protein
KeywordsVIRAL PROTEIN / tailspike protein-protein interaction / TSP4 attachment to the tail baseplate / triple beta-helix / beta jellyroll
Function / homologyTail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Tailspike protein
Function and homology information
Biological speciesEscherichia virus CBA120
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChao, K. / Shang, X. / Grenfield, J. / Linden, S.B. / Nelson, D.C. / Herzberg, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM110202 United States
CitationJournal: Sci Rep / Year: 2022
Title: Structure of Escherichia coli O157:H7 bacteriophage CBA120 tailspike protein 4 baseplate anchor and tailspike assembly domains (TSP4-N).
Authors: Chao, K.L. / Shang, X. / Greenfield, J. / Linden, S.B. / Alreja, A.B. / Nelson, D.C. / Herzberg, O.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tailspike protein


Theoretical massNumber of molelcules
Total (without water)26,6701
Polymers26,6701
Non-polymers00
Water00
1
A: Tailspike protein

A: Tailspike protein

A: Tailspike protein


Theoretical massNumber of molelcules
Total (without water)80,0113
Polymers80,0113
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area15870 Å2
ΔGint-75 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.683, 84.683, 225.073
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Tailspike protein


Mass: 26670.260 Da / Num. of mol.: 1 / Fragment: N-terminal fragment (UNP residues 1-250)
Source method: isolated from a genetically manipulated source
Details: Full-length protein degraded during crystal growth, exact cleavage site unknown
Source: (gene. exp.) Escherichia virus CBA120 / Gene: orf213 / Production host: Escherichia coli (E. coli) / References: UniProt: G3M192

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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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 10.5
Details: 20% w/v PEG8000, 0.2 M sodium chloride, 0.1 M CHAPS, pH 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2020 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→44.64 Å / Num. obs: 7883 / % possible obs: 99 % / Redundancy: 4.6 % / Biso Wilson estimate: 138 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.6
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 3737 / CC1/2: 0.077

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
TRUNCATEdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7REJ

7rej


Resolution: 3.2→29.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 44.77 / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.575 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3008 208 3.9 %RANDOM
Rwork0.2013 ---
obs0.2049 5125 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 250.66 Å2 / Biso mean: 151.627 Å2 / Biso min: 107.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 3.2→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 0 0 1767
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131810
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171560
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.6512487
X-RAY DIFFRACTIONr_angle_other_deg1.1811.5613642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4245239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44724.58372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.04615247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.066154
X-RAY DIFFRACTIONr_chiral_restr0.0460.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022060
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02344
LS refinement shellResolution: 3.2→3.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 23 -
Rwork0.48 347 -
all-370 -
obs--99.73 %

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