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- PDB-1kgm: SOLUTION STRUCTURE OF THE SMALL SERINE PROTEASE INHIBITOR SGCI -

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Entry
Database: PDB / ID: 1kgm
TitleSOLUTION STRUCTURE OF THE SMALL SERINE PROTEASE INHIBITOR SGCI
ComponentsSERINE PROTEASE INHIBITOR I
KeywordsHYDROLASE / Proteinase inhibitor / SGCI
Function / homologyProtease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / serine-type endopeptidase inhibitor activity / extracellular region / Serine protease inhibitor I/II
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsGaspari, Z. / Patthy, A. / Graf, L. / Perczel, A.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Comparative structure analysis of proteinase inhibitors from the desert locust, Schistocerca gregaria.
Authors: Gaspari, Z. / Patthy, A. / Graf, L. / Perczel, A.
History
DepositionNov 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE PROTEASE INHIBITOR I


Theoretical massNumber of molelcules
Total (without water)3,6591
Polymers3,6591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with acceptable covalent geometry,structures with the least restraint violations
RepresentativeModel #5closest to the average

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Components

#1: Protein/peptide SERINE PROTEASE INHIBITOR I / Schistocerca gregaria chymotrypsin inhibitor (SGCI)


Mass: 3659.175 Da / Num. of mol.: 1 / Fragment: Residues 57-91 / Source method: obtained synthetically
Details: Solid-phase synthesis, Fmoc strategy, Sequence naturally found in Schistocerca gregaria (desert locust)
References: UniProt: O46162
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 2.5mM SGCI NA; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 3 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Brungerrefinement
X-PLOR3.851Brungerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures are based on 526 distance restraints (128 long-range)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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