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- PDB-2mm5: solution structure of alpha-amylase inhibitor peptide aS4 from Al... -

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Basic information

Entry
Database: PDB / ID: 2mm5
Titlesolution structure of alpha-amylase inhibitor peptide aS4 from Allatide scholaris
ComponentsAlpha amylase Alstotide S4
KeywordsHYDROLASE INHIBITOR
Function / homologyAlpha amylase Alstotide S4
Function and homology information
Biological speciesAlstonia scholaris (milky pine)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsWang, S. / Nguyen, Q. / Tam, J.
CitationJournal: To be Published
Title: solution structure of alpha-amylase inhibitor peptide aS4 from Allatide scholaris
Authors: Wang, S. / Nguyen, Q. / Tam, J.
History
DepositionMar 10, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references / Source and taxonomy
Revision 1.2Dec 11, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation
Category: pdbx_nmr_sample_details / pdbx_nmr_software ...pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_validate_close_contact / struct_conn
Item: _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha amylase Alstotide S4


Theoretical massNumber of molelcules
Total (without water)3,3261
Polymers3,3261
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Alpha amylase Alstotide S4


Mass: 3325.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: plants / Source: (natural) Alstonia scholaris (milky pine) / References: UniProt: A0A0S0ZR47
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM aS4-1, 95 % H2O-2, 5 % D2O-3, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMaS4-11
95 %H2O-21
5 %D2O-31
Sample conditionsIonic strength: 0 / pH: 3.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRspyZheng Yu, Xu Yingqi and Yang Daiwenchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
MOLMOLKoradi, Billeter and Wuthrichgeometry optimization
ProcheckNMRLaskowski and MacArthurgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 11 / Representative conformer: 1

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