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- PDB-5ujg: ovGRN12-35_3s -

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Basic information

Entry
Database: PDB / ID: 5ujg
TitleovGRN12-35_3s
ComponentsGranulin
KeywordsCYTOKINE / Wound healing agent / granulin / STRUCTURE FROM CYANA 3.97
Function / homologyGranulins signature. / Granulin family / Granulin / Granulin superfamily / Granulin / Granulin / regulation of inflammatory response / extracellular region / Granulin
Function and homology information
Biological speciesOpisthorchis viverrini (Southeast Asian liver fluke)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBansal, P. / Smout, M. / Wilson, D. / Caceres, C.C. / Dastpeyman, M. / Sotillo, J. / Seifert, J. / Brindley, P. / Loukas, A. / Daly, N.
Funding support United States, Australia, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA164719 United States
National Health and Medical Research Council (NHMRC, Australia)1037304 Australia
CitationJournal: J. Med. Chem. / Year: 2017
Title: Development of a Potent Wound Healing Agent Based on the Liver Fluke Granulin Structural Fold.
Authors: Bansal, P.S. / Smout, M.J. / Wilson, D. / Cobos Caceres, C. / Dastpeyman, M. / Sotillo, J. / Seifert, J. / Brindley, P.J. / Loukas, A. / Daly, N.L.
History
DepositionJan 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Granulin


Theoretical massNumber of molelcules
Total (without water)2,5931
Polymers2,5931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Granulin


Mass: 2593.018 Da / Num. of mol.: 1 / Fragment: UNP residues 30-53 / Source method: obtained synthetically
Source: (synth.) Opisthorchis viverrini (Southeast Asian liver fluke)
References: UniProt: B8XSI4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-13C HSQC
131anisotropic12D 1H-1H TOCSY
141anisotropic12D 1H-1H NOESY
151anisotropic12D 1H-1H COSY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM NA ov-GRN12-35_3S peptide, 10 % D2O, 90 % H2O, 90% H2O/10% D2O
Label: 1H_Sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMov-GRN12-35_3S peptideNA1
10 %D2O1
90 %H2O1
Sample conditionsIonic strength units: Not defined / Label: Condition_1 / pH: 5 / Pressure: 1 atm / Temperature: 290 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5PL6Bruker Biospincollection
CcpNMRCCPNdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CcpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 8
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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