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- PDB-6cjz: Solution Structure of Amebosin -

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Basic information

Entry
Database: PDB / ID: 6cjz
TitleSolution Structure of Amebosin
ComponentsAmoebiasin-1
KeywordsPROTEIN FIBRIL / amebosin
Function / homologyProteinase inhibitor I42, chagasin / Chagasin-like superfamily / Chagasin family peptidase inhibitor I42 / cysteine-type endopeptidase inhibitor activity / cytoplasm / Amoebiasin-1
Function and homology information
Biological speciesEntamoeba histolytica (eukaryote)
MethodSOLUTION NMR / na
AuthorsMendoza, A. / Flores-Solis, D. / Del Rio Portilla, F. / Brieba de Castro, L.
Funding support Mexico, 1items
OrganizationGrant numberCountry
DGAPA207516 Mexico
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2020
Title: Solution structure of the inhibitor of cysteine proteases 1 from Entamoeba histolytica reveals a possible auto regulatory mechanism.
Authors: Flores-Solis, D. / Mendoza, A. / Renteria-Gonzalez, I. / Casados-Vazquez, L.E. / Trasvina-Arenas, C.H. / Jimenez-Sandoval, P. / Benitez-Cardoza, C.G. / Del Rio-Portilla, F. / Brieba, L.G.
History
DepositionFeb 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name
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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amoebiasin-1


Theoretical massNumber of molelcules
Total (without water)11,3801
Polymers11,3801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

#1: Protein Amoebiasin-1 / Cysteine protease inhibitor 1 / EhICP1 / ICP-1


Mass: 11379.565 Da / Num. of mol.: 1 / Mutation: C42S, C61S, C63S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: AMS, ICP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6KCA4

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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 NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D DQF-COSY
142isotropic22D 1H-15N HSQC
152isotropic23D 1H-15N NOESY
162isotropic23D 1H-15N TOCSY
173isotropic23D HNCO
183isotropic23D HNCA
193isotropic23D HN(CA)CB
1103isotropic23D HN(CO)CA
1113isotropic23D 1H-15N TOCSY
1123isotropic23D (H)CCH-TOCSY
1133isotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM Amebosin, 95% H2O/5% D2ONatural Label95% H2O/5% D2O
solution21 mM [U-99% 15N] Amebosin, 95% H2O/5% D2ON15 labelled95% H2O/5% D2O
solution31 mM [U-99% 13C; U-99% 15N] Amebosin, 95% H2O/5% D2ODouble labelled95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAmebosinnatural abundance1
1 mMAmebosin[U-99% 15N]2
1 mMAmebosin[U-99% 13C; U-99% 15N]3
Sample conditionsIonic strength: 1 Not defined / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian INOVAVarianINOVA50013mm triple nucleus
Varian VXRSVarianVXRS70025mm Cryoprobe

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: na / Software ordinal: 2 / Details: AutoNOE assignment
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 10

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