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- PDB-1ce3: PUTATIVE ANCESTRAL PROTEIN ENCODED BY A SINGLE SEQUENCE REPEAT OF... -

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Basic information

Entry
Database: PDB / ID: 1ce3
TitlePUTATIVE ANCESTRAL PROTEIN ENCODED BY A SINGLE SEQUENCE REPEAT OF THE MULTIDOMAIN PROTEINASE INHIBITOR FROM NICOTIANA ALATA
ComponentsAPI
KeywordsPROTEASE INHIBITOR / CIRCULAR PERMUTATION / NICOTIANA ALATA
Function / homologyProteinase inhibitor I20 / Potato type II proteinase inhibitor family / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / serine-type endopeptidase inhibitor activity / 2-Layer Sandwich / Alpha Beta / Proteinase inhibitor
Function and homology information
Biological speciesNicotiana alata (Persian tobacco)
MethodSOLUTION NMR / simulated annealing
AuthorsScanlon, M.J. / Lee, M.C.S. / Anderson, M.A. / Craik, D.J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Structure of a putative ancestral protein encoded by a single sequence repeat from a multidomain proteinase inhibitor gene from Nicotiana alata.
Authors: Scanlon, M.J. / Lee, M.C. / Anderson, M.A. / Craik, D.J.
History
DepositionMar 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_nmr_ensemble / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: API


Theoretical massNumber of molelcules
Total (without water)5,9281
Polymers5,9281
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 / 50LEAST RESTRAINT VIOLATIONS AND LOWEST ENERGY
Representative

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Components

#1: Protein API


Mass: 5927.748 Da / Num. of mol.: 1 / Fragment: FIRST SEQUENCE REPEAT
Source method: isolated from a genetically manipulated source
Details: SINGLE SEQUENCE REPEAT FROM A MULTIDOMAIN PROTEINASE INHIBITOR
Source: (gene. exp.) Nicotiana alata (Persian tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: Q40378

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQFCOSY
121ECOSY
131TOCSY
141NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM peptide / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: peptide / Isotopic labeling: natural abundance
Sample conditionspH: 5.8 / Pressure: 1 atm / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7501
Bruker ARXBrukerARX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.85BRUNGERrefinement
XEASYBartels et al.structure calculation
DYANAGuntert, Braun and Wuthrichstructure calculation
X-PLORBRUNGERstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE STRUCTURE CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS AND LOWEST ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 20

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