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- PDB-1ay3: Nodularin from Nodularia spumigena -

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Basic information

Entry
Database: PDB / ID: 1ay3
TitleNodularin from Nodularia spumigena
ComponentsPEPTIDIC TOXIN NODULARIN
KeywordsTOXIN / HEPATOTOXIN / INHIBITOR OF SER/THR-SPECIFIC PROTEIN PHOSPHATASES
Function / homology:
Function and homology information
Biological speciesNodularia spumigena (bacteria)
MethodSOLUTION NMR
AuthorsAnnila, A.J.
CitationJournal: J.Biol.Chem. / Year: 1996
Title: Solution structure of nodularin. An inhibitor of serine/threonine-specific protein phosphatases.
Authors: Annila, A. / Lehtimaki, J. / Mattila, K. / Eriksson, J.E. / Sivonen, K. / Rantala, T.T. / Drakenberg, T.
History
DepositionNov 14, 1997Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Source and taxonomy
Revision 1.4Feb 27, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_polymer_linkage / struct_conn
Item: _pdbx_entry_details.compound_details / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDIC TOXIN NODULARIN


Theoretical massNumber of molelcules
Total (without water)8441
Polymers8441
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)27 / 100RESTRAINT VIOLATIONS
RepresentativeModel #22lowest energy

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Components

#1: Protein/peptide PEPTIDIC TOXIN NODULARIN


Mass: 843.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: TOXIN IS CYCLIC PEPTIDE WITH SEQUENCE 2AS-ARG-MFD-GLU-MDH. ALL PEPTIDIC BONDS ARE NON-STANDARD
Source: (natural) Nodularia spumigena (bacteria) / Strain: BY1 / References: NOR: NOR00279
Compound detailsTHE SEQUENCE OF NODULARIN MATCHES TO THE SEQUENCE OF NOR00279 IN NORINE DATABASE, EXCEPT THAT THE ...THE SEQUENCE OF NODULARIN MATCHES TO THE SEQUENCE OF NOR00279 IN NORINE DATABASE, EXCEPT THAT THE STEREO CHEMISTRY OF RESIDUE MFD IS DIFFERENT FROM THAT OF THE CORRESPONDING RESIDUE 1ZN AS INDICATED AS ADDA IN NOR00279 SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141ROESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TWO-DIMENSIONAL NMR SPECTROSCOPY ON NON-LABELED NODULARIN

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Sample preparation

Sample conditionspH: 4.7 / Pressure: ambient / Temperature: 274 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
IRMABOELENSrefinement
FELIXREMARK 210 METHODMETHODstructure solution
RefinementSoftware ordinal: 1 / Details: ITERATIVE RELAXATION MATRIX ANALYSIS T_C = 1.0 NS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: RESTRAINT VIOLATIONS / Conformers calculated total number: 100 / Conformers submitted total number: 27

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