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- PDB-8vol: Apex domain deletion mutant of bacteriophage P2 central spike pro... -

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Basic information

Entry
Database: PDB / ID: 8vol
TitleApex domain deletion 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: 0.9 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)64,8807
Polymers64,1466
Non-polymers7341
Water21,1861176
1
A: Spike protein
B: Spike protein
C: Spike protein


Theoretical massNumber of molelcules
Total (without water)32,0733
Polymers32,0733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19250 Å2
ΔGint-81 kcal/mol
Surface area13280 Å2
MethodPISA
2
D: Spike protein
E: Spike protein
F: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8074
Polymers32,0733
Non-polymers7341
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20920 Å2
ΔGint-95 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.520, 49.910, 72.930
Angle α, β, γ (deg.)91.610, 88.250, 111.650
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 10691.044 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Exogenous C-terminal leucine was added by mutagenesis.
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.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1176 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
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-D / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 15, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.9→26.73 Å / Num. obs: 821847 / % possible obs: 94.5 % / Redundancy: 3.33 % / Biso Wilson estimate: 7.29 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.083 / Net I/σ(I): 9.69
Reflection shellResolution: 0.9→0.93 Å / Redundancy: 3.15 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 55324 / CC1/2: 0.861 / Rrim(I) all: 0.544 / % possible all: 85.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.9→26.73 Å / SU ML: 0.0611 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 11.8634
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.127 8211 1 %
Rwork0.1163 813076 -
obs0.1164 821287 94.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.6 Å2
Refinement stepCycle: LAST / Resolution: 0.9→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4446 0 50 1176 5672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764916
X-RAY DIFFRACTIONf_angle_d1.07836771
X-RAY DIFFRACTIONf_chiral_restr0.0942874
X-RAY DIFFRACTIONf_plane_restr0.0209863
X-RAY DIFFRACTIONf_dihedral_angle_d8.6824820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.920.22642420.234524000X-RAY DIFFRACTION83.81
0.92-0.930.1842570.204138201X-RAY DIFFRACTION86.94
0.93-0.940.18852480.19425350X-RAY DIFFRACTION89.07
0.94-0.950.20032650.184626021X-RAY DIFFRACTION90.22
0.95-0.960.16822660.172926228X-RAY DIFFRACTION91.1
0.96-0.970.15282630.161726130X-RAY DIFFRACTION91.43
0.97-0.990.17672630.157526394X-RAY DIFFRACTION91.99
0.99-10.13252680.147326373X-RAY DIFFRACTION92.01
1-1.020.14972670.136126586X-RAY DIFFRACTION92.44
1.02-1.040.13192720.124926699X-RAY DIFFRACTION92.76
1.04-1.050.13522690.117526542X-RAY DIFFRACTION92.66
1.05-1.070.12712740.114126934X-RAY DIFFRACTION93.87
1.07-1.090.12192780.110727414X-RAY DIFFRACTION95.74
1.09-1.120.12812770.102127459X-RAY DIFFRACTION95.1
1.12-1.140.10342730.100127015X-RAY DIFFRACTION94.34
1.14-1.170.10972710.098527084X-RAY DIFFRACTION94.32
1.17-1.20.11562860.096228331X-RAY DIFFRACTION98.39
1.2-1.230.10142860.095128247X-RAY DIFFRACTION98.51
1.23-1.260.11852870.096928235X-RAY DIFFRACTION98.54
1.26-1.310.12162860.096828271X-RAY DIFFRACTION98.4
1.31-1.350.10642870.101128264X-RAY DIFFRACTION98.32
1.35-1.410.10542830.099828052X-RAY DIFFRACTION98.19
1.41-1.470.10382850.100428171X-RAY DIFFRACTION97.91
1.47-1.550.10562840.099528000X-RAY DIFFRACTION97.85
1.55-1.640.11042830.100527983X-RAY DIFFRACTION97.39
1.64-1.770.12122820.105427929X-RAY DIFFRACTION97.19
1.77-1.950.11082680.107526698X-RAY DIFFRACTION93.32
1.95-2.230.11932730.104726967X-RAY DIFFRACTION93.61
2.23-2.810.11732850.115728409X-RAY DIFFRACTION98.94
2.81-26.730.15992830.137128156X-RAY DIFFRACTION98.13

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