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- PDB-1htx: SOLUTION STRUCTURE OF THE MAIN ALPHA-AMYLASE INHIBITOR FROM AMARA... -

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Basic information

Entry
Database: PDB / ID: 1htx
TitleSOLUTION STRUCTURE OF THE MAIN ALPHA-AMYLASE INHIBITOR FROM AMARANTH SEEDS
ComponentsALPHA-AMYLASE INHIBITOR AAI
KeywordsPLANT PROTEIN / cysteine knot
Function / homologyalpha-amylase inhibitor activity / Proteinase/amylase inhibitor domain superfamily / endopeptidase inhibitor activity / Alpha-amylase inhibitor AAI
Function and homology information
Biological speciesAmaranthus hypochondriacus (grain amaranth)
MethodSOLUTION NMR / simulated annealing
AuthorsMartins, J.C. / Enassar, M. / Willem, R. / Wieruzeski, J.M. / Lippens, G. / Wodak, S.J.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Solution structure of the main alpha-amylase inhibitor from amaranth seeds.
Authors: Martins, J.C. / Enassar, M. / Willem, R. / Wieruzeski, J.M. / Lippens, G. / Wodak, S.J.
History
DepositionJan 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: ALPHA-AMYLASE INHIBITOR AAI


Theoretical massNumber of molelcules
Total (without water)3,5951
Polymers3,5951
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 / 100structures with favorable non-bond energy,structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein/peptide ALPHA-AMYLASE INHIBITOR AAI


Mass: 3595.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Amaranthus hypochondriacus (grain amaranth)
Organ: SEEDS / References: UniProt: P80403

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
122DQF-COSY
131TOCSY
141TOCSY
1512D NOESY
1622D NOESY
NMR detailsText: This structure was determined from 2D 1H NMR techniques only using the sequence specific resonance assignment procedure, followed by NOE and J data collection, calculation bij X-plor and ...Text: This structure was determined from 2D 1H NMR techniques only using the sequence specific resonance assignment procedure, followed by NOE and J data collection, calculation bij X-plor and refinement with MSI's CVFF forcefield

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM AAI, 0.05 mM NaN390% H2O/10% D2O
21.8 mM AAI, 0.05 mM NaN3100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
12.95 ambient 277 K
22.95 ambient 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AMXBrukerAMX5002
Varian UNITYVarianUNITY6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
VNMRVariancollection
X-PLOR3.1Nilges, M.structure solution
NMR_Refine98MSIrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: restrained MD at 1000K follwed by stepwise cooling to 300K and final restrained energy optimisation
NMR ensembleConformer selection criteria: structures with favorable non-bond energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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