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- PDB-7jiy: Structure of truncated zebrafish paragranulin -

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Basic information

Entry
Database: PDB / ID: 7jiy
TitleStructure of truncated zebrafish paragranulin
ComponentsGranulin 1
KeywordsUNKNOWN FUNCTION / disulfide-rich / growth factor
Function / homologyGranulin family / Granulin / Granulin superfamily / Granulin / Granulin / extracellular region / Granulin 1
Function and homology information
Biological speciesDanio rerio (zebrafish)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTakjoo, R. / Daly, N.L.
CitationJournal: Biomolecules / Year: 2020
Title: Folding of Truncated Granulin Peptides.
Authors: Takjoo, R. / Wilson, D. / Bansal, P.S. / Loukas, A. / Smout, M.J. / Daly, N.L.
History
DepositionJul 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Granulin 1


Theoretical massNumber of molelcules
Total (without water)2,7381
Polymers2,7381
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 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Granulin 1


Mass: 2738.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Danio rerio (zebrafish) / References: UniProt: A8E5C4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H COSY
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 0.2 mM ZF-para_3s, 90% H2O/10% D2O / Label: 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.2 mM / Component: ZF-para_3s / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 M / Label: 1 / pH: 3 / Pressure: ambient Pa / 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
NameDeveloperClassification
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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