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- PDB-6e1l: GRN3Ala -

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Basic information

Entry
Database: PDB / ID: 6e1l
TitleGRN3Ala
ComponentsGranulin
KeywordsCYTOKINE / Wound healing agent / granulin / STRUCTURE FROM CYANA 3.97
Function / homologyGranulins signature. / Granulin family / Granulin / Granulin superfamily / Granulin / Granulin / extracellular region / Granulin
Function and homology information
Biological speciesOpisthorchis viverrini (Southeast Asian liver fluke)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDastpeyman, M. / Bansal, P. / Wilson, D. / Sotillo, J. / Brindley, P. / Loukas, A. / Smout, M. / Daly, N.
Funding support Australia, United States, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)110100226 Australia
National Health and Medical Research Council (NHMRC, Australia)1117504 Australia
National Institutes of Health/National Cancer Institute (NIH/NCI)CA164719 United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structural Variants of a Liver Fluke Derived Granulin Peptide Potently Stimulate Wound Healing.
Authors: Dastpeyman, M. / Bansal, P.S. / Wilson, D. / Sotillo, J. / Brindley, P.J. / Loukas, A. / Smout, M.J. / Daly, N.L.
History
DepositionJul 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: 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 1.2Jun 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)2,5151
Polymers2,5151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2210 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Granulin /


Mass: 2514.907 Da / Num. of mol.: 1 / 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
121anisotropic12D 1H-1H TOCSY
131anisotropic12D 1H-1H COSY
141anisotropic12D 1H-1H NOESY
151anisotropic12D DQF-COSY
161anisotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 0.5 mM NA GRN3Ala, 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 mMGRN3AlaNA1
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 III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5PL6Bruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNMRCCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CcpNMRCCPNdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 15

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