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- PDB-7rfo: SeMet Tailspike protein 4 (TSP4) phage CBA120, residues 1-335, ob... -

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Basic information

Entry
Database: PDB / ID: 7rfo
TitleSeMet Tailspike protein 4 (TSP4) phage CBA120, residues 1-335, obtained in the presence of LiSO4
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 / SAD / Resolution: 3.02 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 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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


Theoretical massNumber of molelcules
Total (without water)109,9693
Polymers109,9693
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17340 Å2
ΔGint-99 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.900, 67.900, 607.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Tailspike protein / Tailspike protein 4


Mass: 36656.230 Da / Num. of mol.: 3 / Fragment: N-terminal domain (UNP residues 1-335) / Mutation: L12M, I31M, L145M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus CBA120 / Gene: orf213 / Production host: Escherichia coli (E. coli) / References: UniProt: G3M192
Has ligand of interestN
Has protein modificationY

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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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 1.6 M lithium sulfate, 0.1 M sodium chloride, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 15, 2020 / Details: mirrors
RadiationMonochromator: double crystal monochromato / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.02→48.01 Å / Num. obs: 28173 / % possible obs: 94.4 % / Redundancy: 66.9 % / Biso Wilson estimate: 119.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.228 / Net I/σ(I): 20.4
Reflection shellResolution: 3.02→3.2 Å / Num. unique obs: 3193 / CC1/2: 0.256

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACTdata extraction
TRUNCATEdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.02→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.903 / SU B: 58.21 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2956 1370 4.9 %RANDOM
Rwork0.2249 ---
obs0.2281 26761 94.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 324.53 Å2 / Biso mean: 141.892 Å2 / Biso min: 72.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2--2.13 Å20 Å2
3----4.26 Å2
Refinement stepCycle: final / Resolution: 3.02→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7073 0 0 0 7073
Num. residues----983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137243
X-RAY DIFFRACTIONr_bond_other_d0.0070.0176107
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.6529934
X-RAY DIFFRACTIONr_angle_other_deg1.5351.56414237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6775979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57224.389303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.34415915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1461521
X-RAY DIFFRACTIONr_chiral_restr0.0740.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028416
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021407
LS refinement shellResolution: 3.02→3.094 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.53 55 -
Rwork0.455 937 -
obs--45.8 %
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)
14.2112-0.9698-1.8153.56072.53233.8585-0.18710.0802-0.18420.02980.05660.0069-0.1109-0.17270.13040.1068-0.04210.16710.0678-0.13710.366230.86374.354288.923
22.04730.0624-0.50263.57931.42796.22260.08970.6113-0.073-1.09170.0428-0.0008-0.09560.4401-0.13250.37040.04010.03990.2891-0.17310.411149.32757.618247.449
36.321-1.0254-1.07580.9-0.4741.1496-0.0906-0.0345-0.21610.0384-0.0199-0.28210.04480.26420.11060.0655-0.02320.05520.1916-0.19430.392771.12455.926270.452
40.8617-1.63890.24536.88610.51071.0990.0460.1403-0.2209-0.0605-0.15660.12030.16990.06420.11060.084-0.04710.1280.0828-0.14330.328247.58934.114268.607
50.01630.0277-0.01280.082-0.02480.01210.0448-0.0051-0.1336-0.0664-0.1454-0.2928-0.04830.05320.10061.0764-0.01050.05371.39920.06131.284277.04622.756255.61
63.6669-3.97140.81634.9257-1.20680.3781-0.1215-0.3574-0.3823-0.78490.0451-0.09320.5448-0.07010.07641.6705-0.06260.44231.58290.05342.145959.22625.853239.898
71.5610.09530.20790.00640.01280.040.1269-0.2901-0.06340.0117-0.0458-0.00870.1329-0.0265-0.08121.629-0.0919-0.1121.3810.06151.153376.80340.481239.158
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 79
2X-RAY DIFFRACTION1B1 - 79
3X-RAY DIFFRACTION1C1 - 79
4X-RAY DIFFRACTION2A80 - 255
5X-RAY DIFFRACTION3B80 - 255
6X-RAY DIFFRACTION4C80 - 255
7X-RAY DIFFRACTION5A256 - 337
8X-RAY DIFFRACTION6B256 - 336
9X-RAY DIFFRACTION7C256 - 336

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