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- PDB-1g26: THE SOLUTION STRUCTURE OF A WELL-FOLDED PEPTIDE BASED ON THE 31-R... -

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Basic information

Entry
Database: PDB / ID: 1g26
TitleTHE SOLUTION STRUCTURE OF A WELL-FOLDED PEPTIDE BASED ON THE 31-RESIDUE AMINO-TERMINAL SUBDOMAIN OF HUMAN GRANULIN A
ComponentsGRANULIN A
KeywordsCYTOKINE / granulin/epithelin protein repeats / beta-hairpin stack
Function / homology
Function and homology information


positive regulation of aspartic-type peptidase activity / positive regulation of inflammatory response to wounding / negative regulation of neutrophil activation / positive regulation of protein folding / microglial cell activation involved in immune response / positive regulation of lysosome organization / positive regulation of defense response to bacterium / negative regulation of microglial cell activation / lysosomal lumen acidification / astrocyte activation involved in immune response ...positive regulation of aspartic-type peptidase activity / positive regulation of inflammatory response to wounding / negative regulation of neutrophil activation / positive regulation of protein folding / microglial cell activation involved in immune response / positive regulation of lysosome organization / positive regulation of defense response to bacterium / negative regulation of microglial cell activation / lysosomal lumen acidification / astrocyte activation involved in immune response / lysosomal transport / lysosome organization / positive regulation of axon regeneration / negative regulation of respiratory burst involved in inflammatory response / positive regulation of endothelial cell migration / cytokine activity / positive regulation of epithelial cell proliferation / growth factor activity / trans-Golgi network / positive regulation of angiogenesis / azurophil granule lumen / positive regulation of neuron apoptotic process / late endosome / protein-folding chaperone binding / regulation of inflammatory response / negative regulation of neuron apoptotic process / lysosome / protein stabilization / endosome / positive regulation of cell migration / lysosomal membrane / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / signal transduction / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Granulins signature. / Granulin family / Granulin / Granulin superfamily / Granulin / Granulin
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsTolkatchev, D. / Ng, A. / Vranken, W. / Ni, F.
CitationJournal: Biochemistry / Year: 2000
Title: Design and solution structure of a well-folded stack of two beta-hairpins based on the amino-terminal fragment of human granulin A.
Authors: Tolkatchev, D. / Ng, A. / Vranken, W. / Ni, F.
History
DepositionOct 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRANULIN A


Theoretical massNumber of molelcules
Total (without water)3,3941
Polymers3,3941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations
Representative

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Components

#1: Protein/peptide GRANULIN A / HGA


Mass: 3393.955 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN (RESIDUES 1-31) / Mutation: D1V, K3H, S9I, Q20P / Source method: obtained synthetically
Details: The peptide was chemically synthesized using standard Fmoc chemistry and oxidized by air in solution, Cys17 and Cys27 were blocked with S-acetamidomethyl groups (Acm)
References: UniProt: P28799

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
1322D NOESY
2422D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM HGA 1-31 (D1V, K3H, S9I, Q20P); 20 mM sodium acetate-d3, 10% D2O, 90% H2O10% D2O, 90% H2O
20.5 mM HGA 1-31 (D1V, K3H, S9I, Q20P); 20 mM sodium acetate-d3, 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.0 ambient 288 K
25.0 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerrefinement
X-PLOR3.1Brungerstructure solution
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 241 restraints, 174 are unambiguous NOE-derived distance constraints, 47 ambiguous NOE-derived distance constraints, 8 dihedral angle restraints, 10 ...Details: The structures are based on a total of 241 restraints, 174 are unambiguous NOE-derived distance constraints, 47 ambiguous NOE-derived distance constraints, 8 dihedral angle restraints, 10 distance restraints from hydrogen bonds, 2 distance restraints from disulfide bonds.
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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