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- PDB-1fa3: SOLUTION STRUCTURE OF MNEI, A SWEET PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1fa3
TitleSOLUTION STRUCTURE OF MNEI, A SWEET PROTEIN
ComponentsMNEI SWEET PROTEIN RELATED TO MONELLIN
KeywordsSTRUCTURAL PROTEIN / 5 stranded beta sheet 1 helix
Function / homology
Function and homology information


Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodSOLUTION NMR / torsion angle dynamics energy restrained minimization
AuthorsTemussi, P.A. / Spadaccini, R.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structure of a sweet protein: NMR study of MNEI, a single chain monellin.
Authors: Spadaccini, R. / Crescenzi, O. / Tancredi, T. / De Casamassimi, N. / Saviano, G. / Scognamiglio, R. / Di Donato, A. / Temussi, P.A.
History
DepositionJul 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2000Provider: 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: 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: MNEI SWEET PROTEIN RELATED TO MONELLIN


Theoretical massNumber of molelcules
Total (without water)11,2881
Polymers11,2881
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)20 / 40structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Representative

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Components

#1: Protein MNEI SWEET PROTEIN RELATED TO MONELLIN


Mass: 11287.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
Plasmid: PET-22B+ / Production host: Escherichia coli (E. coli) / References: UniProt: P02882, UniProt: P02881

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
131HSQC
141HNHB
353E-COSY
3632D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM MNEI U-15N; 18.5mM phosphate buffer K; 90% H2O, 10% D2O90% H2O/10% D2O
22mM MNEI; 18.5mM phosphate buffer K; 90% H2O, 10% D2O90% H2O/10% D2O
32mM MNEI; 18.5mM phosphate buffer; 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
118.5 mM phosphate buffer 2.9 ambient 308 K
218.5 mM phosphate buffer 2.9 ambient 308 K
318.5 mM phosphate buffer 2.9 ambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7Delaglioprocessing
DYANA1.5Guentertstructure solution
Amber5Kollmanrefinement
RefinementMethod: torsion angle dynamics energy restrained minimization
Software ordinal: 1
Details: the structures are based on a total of 1169 distance constraints, 184 dihedral angle restraints and 60 distance restraints from hydrogen bonds.
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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