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- PDB-1fwo: THE SOLUTION STRUCTURE OF A 35-RESIDUE FRAGMENT FROM THE GRANULIN... -

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Basic information

Entry
Database: PDB / ID: 1fwo
TitleTHE SOLUTION STRUCTURE OF A 35-RESIDUE FRAGMENT FROM THE GRANULIN/EPITHELIN-LIKE SUBDOMAIN OF RICE ORYZAIN BETA (ROB 382-416 (C398S,C399S,C407S,C413S))
ComponentsORYZAIN BETA CHAIN
KeywordsHYDROLASE / beta-hairpin stack fold / granulin/epithelin-like protein repeats
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Granulin / Granulin superfamily / Granulin / Granulin / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. ...Granulin / Granulin superfamily / Granulin / Granulin / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsTolkatchev, D. / Xu, P. / Ni, F.
CitationJournal: J.Pept.Res. / Year: 2001
Title: A peptide derived from the C-terminal part of a plant cysteine protease folds into a stack of two beta-hairpins, a scaffold present in the emerging family of granulin-like growth factors.
Authors: Tolkatchev, D. / Xu, P. / Ni, F.
History
DepositionSep 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: 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_software ...database_2 / pdbx_nmr_software / 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_software.name / _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: ORYZAIN BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)3,7111
Polymers3,7111
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 ORYZAIN BETA CHAIN


Mass: 3711.060 Da / Num. of mol.: 1
Fragment: C-TERMINAL GRANULIN/EPITHELIN-LIKE EXTENSION (RESIDUES 382-416)
Mutation: C398S,C399S,C407S,C413S / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide naturally occurs in Oryza sativa (rice).
References: UniProt: P25777, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1232D 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 ROB 382-416 (C398S,C399S,C407S,C413S), 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM ROB 382-416 (C398S,C399S,C407S,C413S), 20 mM sodium acetate-d3, 90% H2O, 10% D2O90% H2O/10% D2O
30.5 mM ROB 382-416 (C398S,C399S,C407S,C413S), 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 2.0 ambient 288 K
20.02 5.0 ambient 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerrefinement
UXNMR2.1Brukerprocessing
Pronto19990105Kjaer, M., Andersen, K.V., Poulsen, F. M.data analysis
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 288 restraints, 195 are unambiguous NOE-derived distance constraints, 91 ambiguous NOE-derived distance constraints, 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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