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- PDB-7qab: NMR Solution Structure of mussel adhesive protein Pvfp-5b -

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Basic information

Entry
Database: PDB / ID: 7qab
TitleNMR Solution Structure of mussel adhesive protein Pvfp-5b
ComponentsPVFP-5
KeywordsSTRUCTURAL PROTEIN / adhesion proteins / bioadhesives / mussel foot proteins / coacervation
Function / homologyEGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / PVFP-5
Function and homology information
Biological speciesPerna viridis (Asian green mussel)
MethodSOLUTION NMR / simulated annealing
AuthorsMorando, M.A. / Venturella, F. / Pastore, A. / Alfano, C.
Funding support2items
OrganizationGrant numberCountry
Other governmentCUP G77B17000110001
Other governmentCUP G76G17000130007
Citation
Journal: Commun Biol / Year: 2022
Title: Solution structure of recombinant Pvfp-5 beta reveals insights into mussel adhesion.
Authors: Morando, M.A. / Venturella, F. / Sollazzo, M. / Monaca, E. / Sabbatella, R. / Vetri, V. / Passantino, R. / Pastore, A. / Alfano, C.
#1: Journal: J Biol Chem / Year: 2019
Title: Recombinant mussel protein Pvfp-5b: A potential tissue bioadhesive.
Authors: Santonocito, R. / Venturella, F. / Dal Piaz, F. / Morando, M.A. / Provenzano, A. / Rao, E. / Costa, M.A. / Bulone, D. / San Biagio, P.L. / Giacomazza, D. / Sicorello, A. / Alfano, C. / ...Authors: Santonocito, R. / Venturella, F. / Dal Piaz, F. / Morando, M.A. / Provenzano, A. / Rao, E. / Costa, M.A. / Bulone, D. / San Biagio, P.L. / Giacomazza, D. / Sicorello, A. / Alfano, C. / Passantino, R. / Pastore, A.
History
DepositionNov 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PVFP-5


Theoretical massNumber of molelcules
Total (without water)9,5151
Polymers9,5151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein PVFP-5


Mass: 9514.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Perna viridis (Asian green mussel) / Production host: Escherichia coli (E. coli) / References: UniProt: U5Y6P4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic12D (HB)CB(CGCD)HD
142isotropic12D (HB)CB(CGCDCE)HE
151isotropic13D HNCO
161isotropic13D HNCA
181isotropic13D HN(CO)CA
192isotropic13D HN(COCA)CB
1102isotropic13D HN(CA)CB
1112isotropic13D HBHA(CO)NH
1122isotropic13D HBHANH
1132isotropic13D 1H-13C NOESY aliphatic
1142isotropic13D 1H-13C NOESY aromatic
1152isotropic13D 1H-15N NOESY
1162isotropic13D (H)CCH-TOCSY aliphatic
1171isotropic23D (H)CCH-TOCSY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM [U-100% 13C; U-100% 15N] Pvfp-5b, 20 mM sodium acetate pH 4.5, 90% H2O/10% D2O15N13C_Pvfp5b_190% H2O/10% D2O
solution2900 uM [U-100% 13C; U-100% 15N] pvfp5b, 20 mM sodium acetate pH 4.5, 90% H2O/10% D2O15N13C_Pvfp5b_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMPvfp-5b[U-100% 13C; U-100% 15N]1
20 mMsodium acetate pH 4.5natural abundance1
900 uMpvfp5b[U-100% 13C; U-100% 15N]2
20 mMsodium acetate pH 4.5natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1NA Not definedcondition 14.5 1 atm298 K
2NA Not definedcondition 14.5 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE NEOBrukerAVANCE NEO8001Ri.MED Foundation
Bruker AVANCE III HDBrukerAVANCE III HD7002MRC Biomedical NMR Centre

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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