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- PDB-7rej: Tailspike protein 4 (TSP4) from phage CBA120, residues 1-335, obt... -

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Basic information

Entry
Database: PDB / ID: 7rej
TitleTailspike protein 4 (TSP4) from phage CBA120, residues 1-335, obtained in the presence of NaK-Tartrate
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 / IMIDAZOLE / Tailspike protein
Function and homology information
Biological speciesEscherichia virus CBA120
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,7804
Polymers72,6422
Non-polymers1382
Water55831
1
A: Tailspike protein
hetero molecules

A: Tailspike protein
hetero molecules

A: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1706
Polymers108,9623
Non-polymers2073
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-y-2,x-y,z1
crystal symmetry operation3_335-x+y-2,-x-2,z1
Buried area18360 Å2
ΔGint-82 kcal/mol
Surface area42300 Å2
MethodPISA
2
B: Tailspike protein
hetero molecules

B: Tailspike protein
hetero molecules

B: Tailspike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1706
Polymers108,9623
Non-polymers2073
Water543
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 area15320 Å2
ΔGint-68 kcal/mol
Surface area33140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.030, 78.030, 326.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-512-

HOH

31A-514-

HOH

41B-504-

HOH

51B-510-

HOH

61B-511-

HOH

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Components

#1: Protein Tailspike protein


Mass: 36320.750 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-335)
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
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.8
Details: 1 M potassium sodium tartrate, 0.2 M sodium chloride, 0.1 M imidazole, pH 7.8

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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 3, 2018 / Details: mirrors
RadiationMonochromator: double crystal monochromato / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→27.37 Å / Num. obs: 25427 / % possible obs: 98.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 52 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.1
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.85 / Num. unique obs: 2897 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet TSP4-N(1-335) structure

Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 26.051 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.554 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1117 5 %RANDOM
Rwork0.2045 ---
obs0.2056 21436 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.16 Å2 / Biso mean: 80.295 Å2 / Biso min: 29.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å20 Å2
3----2.36 Å2
Refinement stepCycle: final / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4281 0 10 31 4322
Biso mean--59.4 51.59 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134392
X-RAY DIFFRACTIONr_bond_other_d0.0060.0173846
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.656016
X-RAY DIFFRACTIONr_angle_other_deg1.5091.5638976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7955573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86424190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.38815629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1941515
X-RAY DIFFRACTIONr_chiral_restr0.090.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.025020
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02861
LS refinement shellResolution: 2.6→2.666 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 64 -
Rwork0.336 1575 -
all-1639 -
obs--98.91 %
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)
11.7202-0.99751.13692.2007-0.11216.4207-0.0835-0.3289-0.03090.5077-0.0547-0.2886-0.17420.40420.13810.3638-0.0621-0.0070.43450.03670.1247-73.825-44.263-70.351
21.84920.6446-0.82814.0637-1.7981.86430.0592-0.3524-0.11940.4554-0.1471-0.3217-0.17370.250.0880.0594-0.0023-0.03350.0994-0.00950.1187-64.813-57.03-25.21
33.4474-0.4274-0.29897.7702-2.01574.2612-0.049-0.2096-0.03980.4969-0.0069-0.5232-0.0260.21390.0560.5538-0.0231-0.07030.73230.02610.8504-65.155-40.6585.861
42.21250.3028-0.77633.0405-2.37465.682-0.1-0.0520.2078-0.0547-0.1462-0.0775-0.06780.09210.24610.0430.0198-0.02170.0196-0.0060.0401-36.906-18.65-6.404
54.27170.99670.27034.36490.87242.3393-0.14140.9620.2161-1.00440.11390.6012-0.2579-0.27050.02740.28030.0241-0.07490.28440.04870.2333-54.495-13.657-54.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 75
2X-RAY DIFFRACTION2A76 - 256
3X-RAY DIFFRACTION3A265 - 335
4X-RAY DIFFRACTION4B4 - 75
5X-RAY DIFFRACTION5B76 - 255

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