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- PDB-8von: Double phenylalanine Apex domain mutant of bacteriophage P2 centr... -

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Basic information

Entry
Database: PDB / ID: 8von
TitleDouble phenylalanine 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: 1.15 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)72,9057
Polymers72,1716
Non-polymers7341
Water16,970942
1
A: Spike protein
B: Spike protein
C: Spike protein


  • defined by author&software
  • 36.1 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)36,0853
Polymers36,0853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18630 Å2
ΔGint-77 kcal/mol
Surface area13120 Å2
MethodPISA
2
D: Spike protein
E: Spike protein
F: Spike protein
hetero molecules


  • defined by author&software
  • 36.8 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)36,8194
Polymers36,0853
Non-polymers7341
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20530 Å2
ΔGint-92 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.570, 49.510, 89.540
Angle α, β, γ (deg.)106.490, 89.740, 112.340
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: 12028.461 Da / Num. of mol.: 6 / Mutation: H197F, H199F
Source method: isolated from a genetically manipulated source
Details: Disordered C-terminus / 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.: 942 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
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: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 3, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 489332 / % possible obs: 98.7 % / Redundancy: 4.81 % / Biso Wilson estimate: 10.75 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.076 / Net I/σ(I): 13.62
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 4.33 % / Mean I/σ(I) obs: 5.55 / Num. unique obs: 34586 / CC1/2: 0.96 / Rrim(I) all: 0.267 / % possible all: 94

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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: 1.15→34.77 Å / SU ML: 0.0628 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 9.5751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1276 7338 1.5 %
Rwork0.1143 481854 -
obs0.1145 489192 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.4 Å2
Refinement stepCycle: LAST / Resolution: 1.15→34.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 0 50 942 5355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924704
X-RAY DIFFRACTIONf_angle_d1.09776442
X-RAY DIFFRACTIONf_chiral_restr0.0997828
X-RAY DIFFRACTIONf_plane_restr0.023815
X-RAY DIFFRACTIONf_dihedral_angle_d8.2955751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.14052100.121214113X-RAY DIFFRACTION86.83
1.16-1.170.12012480.10916227X-RAY DIFFRACTION99.82
1.17-1.190.1382480.106816185X-RAY DIFFRACTION99.76
1.19-1.20.12882470.10316347X-RAY DIFFRACTION99.82
1.2-1.220.11132440.099816027X-RAY DIFFRACTION99.75
1.22-1.230.11482520.099516428X-RAY DIFFRACTION99.7
1.23-1.250.1262440.096716048X-RAY DIFFRACTION99.73
1.25-1.270.12882500.095716364X-RAY DIFFRACTION99.66
1.27-1.290.09782460.09316109X-RAY DIFFRACTION99.57
1.29-1.310.11212460.096816157X-RAY DIFFRACTION99.51
1.31-1.330.13392490.099316311X-RAY DIFFRACTION99.52
1.33-1.360.12942440.097716012X-RAY DIFFRACTION99.05
1.36-1.380.09952440.093716143X-RAY DIFFRACTION99.03
1.38-1.410.11022420.095915836X-RAY DIFFRACTION97.57
1.41-1.440.11382410.092215938X-RAY DIFFRACTION98.13
1.44-1.480.10232480.087316313X-RAY DIFFRACTION99.96
1.48-1.510.112480.084116328X-RAY DIFFRACTION99.96
1.51-1.560.10272480.085516166X-RAY DIFFRACTION99.95
1.56-1.60.11452480.083416234X-RAY DIFFRACTION99.55
1.6-1.650.12480.087516291X-RAY DIFFRACTION99.92
1.65-1.710.1052480.089916242X-RAY DIFFRACTION99.81
1.71-1.780.11152450.094216161X-RAY DIFFRACTION99.79
1.78-1.860.1142450.099416216X-RAY DIFFRACTION99.65
1.86-1.960.10942480.097116184X-RAY DIFFRACTION99.41
1.96-2.080.11192470.098316128X-RAY DIFFRACTION99.06
2.08-2.240.12132440.107416030X-RAY DIFFRACTION98.74
2.24-2.470.10792380.115515670X-RAY DIFFRACTION96.32
2.47-2.830.14722440.127215979X-RAY DIFFRACTION98.31
2.83-3.560.15072450.132116035X-RAY DIFFRACTION98.38
3.56-34.770.16362390.170915632X-RAY DIFFRACTION96.29

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