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- PDB-7x77: Ectodomain structure of per os infectivity factor 5 -

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Basic information

Entry
Database: PDB / ID: 7x77
TitleEctodomain structure of per os infectivity factor 5
ComponentsPer os infectivity factor 5
KeywordsMEMBRANE PROTEIN / Baculovirus / per os infectivity factors / Cell entry
Function / homologyBaculovirus occlusion-derived virus envelope, E56 / Baculoviral E56 protein, specific to ODV envelope / membrane => GO:0016020 / viral envelope / Occlusion-derived virus envelope protein
Function and homology information
Biological speciesAutographa californica multiple nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsCao, S. / Li, Z. / Fu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDJ-SSW-SMC021 China
CitationJournal: J.Virol. / Year: 2022
Title: Structural Characterization of Per Os Infectivity Factor 5 (PIF5) Reveals the Essential Role of Intramolecular Interactions in Baculoviral Oral Infectivity.
Authors: Li, Z. / Zhang, H. / Li, Z. / Fu, Y. / Wang, X. / Li, J. / Wang, K. / Wang, Z. / Zhang, T. / Wang, M. / Hu, Z. / Cao, S.
History
DepositionMar 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Per os infectivity factor 5


Theoretical massNumber of molelcules
Total (without water)41,3391
Polymers41,3391
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14810 Å2
Unit cell
Length a, b, c (Å)68.173, 92.360, 52.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Per os infectivity factor 5 / Occlusion-derived virus envelope protein


Mass: 41339.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica multiple nucleopolyhedrovirus
Gene: Ac-odv-e56, LO84_150 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0N7CNF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
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: 2 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M BICINE, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→46.18 Å / Num. obs: 17363 / % possible obs: 99.8 % / Redundancy: 12.8 % / Biso Wilson estimate: 25.18 Å2 / Rmerge(I) obs: 0.1392 / Net I/σ(I): 12.94
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.4548 / Num. unique obs: 1673

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Processing

Software
NameVersionClassification
XDSdata reduction
autoSHARPphasing
PHENIXmodel building
Cootmodel building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.18 Å / SU ML: 0.2337 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.9875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 869 5.01 %
Rwork0.1987 16490 -
obs0.2011 17359 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.39 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 0 91 2450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652411
X-RAY DIFFRACTIONf_angle_d0.7713289
X-RAY DIFFRACTIONf_chiral_restr0.0476365
X-RAY DIFFRACTIONf_plane_restr0.0062447
X-RAY DIFFRACTIONf_dihedral_angle_d5.5545328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.30161400.21532651X-RAY DIFFRACTION99.01
2.34-2.520.26461430.22122719X-RAY DIFFRACTION99.93
2.52-2.780.26051430.22722712X-RAY DIFFRACTION99.96
2.78-3.180.26191440.22342731X-RAY DIFFRACTION100
3.18-40.27341460.19592779X-RAY DIFFRACTION100
4-46.180.18851530.16762898X-RAY DIFFRACTION99.97

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