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- PDB-8s9e: Solution structure of jarastatin (rJast), a disintegrin from Both... -

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Basic information

Entry
Database: PDB / ID: 8s9e
TitleSolution structure of jarastatin (rJast), a disintegrin from Bothrops jararaca
ComponentsDisintegrin jarastatin
KeywordsTOXIN / Protein / Disintegrin
Function / homology
Function and homology information


chemotaxis / toxin activity / apoptotic process / extracellular region
Similarity search - Function
Disintegrin, conserved site / Disintegrins signature. / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily
Similarity search - Domain/homology
Disintegrin jarastatin
Similarity search - Component
Biological speciesBothrops jararaca (jararaca)
MethodSOLUTION NMR / molecular dynamics
AuthorsVasconcelos, A.A. / Estrada, J.E.C. / Zingali, R.B. / Almeida, F.C.L.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)313517/2021-5 Brazil
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Toward the mechanism of jarastatin (rJast) inhibition of the integrin alpha V beta 3.
Authors: Vasconcelos, A.A. / Estrada, J.C. / Caruso, I.P. / Kurtenbach, E. / Zingali, R.B. / Almeida, F.C.L.
History
DepositionMar 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author / database_2
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disintegrin jarastatin


Theoretical massNumber of molelcules
Total (without water)7,7621
Polymers7,7621
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Disintegrin jarastatin


Mass: 7761.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bothrops jararaca (jararaca) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q0NZX5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic13D HNCA
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HNCO
171isotropic1HN(CA)CO
181isotropic2HBHA(CO)NH
191isotropic2(H)CCH-TOCSY
1101isotropic215N NOESY-HSQC
1111isotropic213C NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 800 uM [U-100% 13C; U-100% 15N] rJAST, 90% H2O/10% D2O
Details: 5 mM sodium phosphate buffer pH 6.0 / Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 800 uM / Component: rJAST / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 5 mM / Ionic strength err: 0.1 / Label: conditions_1 / pH: 6.0 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE III HDBrukerAVANCE III HD9002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
NMRPipe2022.311.13.21Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.5.2CCPNchemical shift assignment
TopSpin3.5Bruker Biospincollection
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 2 / Details: Water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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