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- PDB-8vom: Double alanine Apex domain mutant of bacteriophage P2 central spi... -

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Basic information

Entry
Database: PDB / ID: 8vom
TitleDouble alanine Apex domain mutant of bacteriophage P2 central spike protein, membrane-piercing module
ComponentsSpike protein
KeywordsVIRAL PROTEIN / Membrane-piercing / phage / baseplate / trimer
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / symbiont genome entry into host cell via pore formation in plasma membrane / entry receptor-mediated virion attachment to host cell / metal ion binding
Similarity search - Function
Phage spike trimer / Phage spike trimer / Phage baseplate assembly protein V/Gp45 / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Spike protein
Similarity search - Component
Biological speciesBacteriophage P2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsLeiman, P.G. / Miller, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM139034 United States
CitationJournal: bioRxiv / Year: 2023
Title: Function of the bacteriophage P2 baseplate central spike Apex domain in the infection process.
Authors: Miller, J.M. / Knyazhanskaya, E.S. / Buth, S.A. / Prokhorov, N.S. / Leiman, P.G.
History
DepositionJan 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein
B: Spike protein
C: Spike protein
D: Spike protein
E: Spike protein
F: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7268
Polymers71,2586
Non-polymers1,4682
Water14,520806
1
A: Spike protein
B: Spike protein
C: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3634
Polymers35,6293
Non-polymers7341
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20570 Å2
ΔGint-89 kcal/mol
Surface area11760 Å2
MethodPISA
2
D: Spike protein
E: Spike protein
F: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3634
Polymers35,6293
Non-polymers7341
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20600 Å2
ΔGint-93 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.010, 52.810, 78.370
Angle α, β, γ (deg.)90.000, 108.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Spike protein / Baseplate assembly protein gpV / Gene V protein / GpV


Mass: 11876.268 Da / Num. of mol.: 6 / Mutation: H197A, H199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage P2 (virus) / Strain: Vir1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31340
#2: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 26-33% Pentaerythritol ethoxylate (15/4 EO/OH) aka PEE-797, 100 mM Bis-Tris or MES pH 6.0-6.5
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2021
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 306387 / % possible obs: 99.7 % / Redundancy: 7.42 % / Biso Wilson estimate: 12.55 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.064 / Net I/σ(I): 18.03
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 7.16 % / Mean I/σ(I) obs: 5.24 / Num. unique obs: 22084 / CC1/2: 0.959 / Rrim(I) all: 0.483 / % possible all: 97.2

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Processing

Software
NameVersionClassification
XDS1.20.1_4487data reduction
XSCALE1.20.1_4487data scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→44.06 Å / SU ML: 0.0799 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 12.6145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1391 6089 1.99 %
Rwork0.119 299175 -
obs0.1194 305264 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.66 Å2
Refinement stepCycle: LAST / Resolution: 1.25→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 100 806 5208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774664
X-RAY DIFFRACTIONf_angle_d1.01046372
X-RAY DIFFRACTIONf_chiral_restr0.0872816
X-RAY DIFFRACTIONf_plane_restr0.0187805
X-RAY DIFFRACTIONf_dihedral_angle_d10.4782767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.22931930.16539356X-RAY DIFFRACTION93.83
1.27-1.280.16142070.139310013X-RAY DIFFRACTION99.9
1.28-1.30.1382040.13169994X-RAY DIFFRACTION99.99
1.3-1.310.14352000.126610029X-RAY DIFFRACTION99.99
1.31-1.330.17052050.130110009X-RAY DIFFRACTION99.98
1.33-1.350.16742020.13059985X-RAY DIFFRACTION99.99
1.35-1.370.16952030.12579966X-RAY DIFFRACTION100
1.37-1.390.1422070.126610060X-RAY DIFFRACTION100
1.39-1.410.14182060.12510029X-RAY DIFFRACTION100
1.41-1.430.15322010.117310003X-RAY DIFFRACTION99.99
1.43-1.460.15652020.11549944X-RAY DIFFRACTION99.94
1.46-1.480.142030.10169944X-RAY DIFFRACTION99.93
1.48-1.510.12792030.097310035X-RAY DIFFRACTION99.99
1.51-1.540.1262020.09549985X-RAY DIFFRACTION99.99
1.54-1.580.12462020.086110041X-RAY DIFFRACTION99.98
1.58-1.610.11142020.09179962X-RAY DIFFRACTION99.95
1.61-1.650.12182030.093510039X-RAY DIFFRACTION99.99
1.65-1.70.1532020.099310020X-RAY DIFFRACTION99.95
1.7-1.750.12282050.09899976X-RAY DIFFRACTION99.97
1.75-1.80.1192030.100210001X-RAY DIFFRACTION99.9
1.8-1.870.12922040.10159988X-RAY DIFFRACTION99.92
1.87-1.940.11222060.093310001X-RAY DIFFRACTION99.99
1.94-2.030.1212030.09279968X-RAY DIFFRACTION99.91
2.03-2.140.11032050.104310013X-RAY DIFFRACTION99.95
2.14-2.270.12342010.10429986X-RAY DIFFRACTION99.95
2.27-2.450.11332020.108410016X-RAY DIFFRACTION99.91
2.45-2.70.13732040.1199970X-RAY DIFFRACTION99.89
2.7-3.080.14512010.13119987X-RAY DIFFRACTION99.95
3.09-3.890.15222060.12669988X-RAY DIFFRACTION99.84
3.89-44.060.1742020.17299867X-RAY DIFFRACTION98.45

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