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- PDB-2jue: Solution structure of the all-D kalata B1 -

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Basic information

Entry
Database: PDB / ID: 2jue
TitleSolution structure of the all-D kalata B1
ComponentsKalata-B1
KeywordsAntibiotic / plant protein / cystine knot / D-amino acid / beta hairpin / cyclic backbone / UNKNOWN FUNCTION
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium
Similarity search - Function
Cyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family
Similarity search - Domain/homology
ALL-D KALATA B1 / Kalata-B1
Similarity search - Component
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDaly, N.L. / Sando, L. / Craik, D.
CitationJournal: Chembiochem / Year: 2011
Title: A Synthetic mirror image of kalata B1 reveals that cyclotide activity is independent of a protein receptor.
Authors: Sando, L. / Henriques, S.T. / Foley, F. / Simonsen, S.M. / Daly, N.L. / Hall, K.N. / Gustafson, K.R. / Aguilar, M.I. / Craik, D.J.
History
DepositionAug 23, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 19, 2015Group: Database references
Revision 2.0Aug 12, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / pdbx_entity_src_syn / pdbx_molecule_features / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kalata-B1


Theoretical massNumber of molelcules
Total (without water)2,9171
Polymers2,9171
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Kalata-B1


Type: Cyclic peptide / Class: Antimicrobial, Antitumor / Mass: 2917.345 Da / Num. of mol.: 1 / Fragment: residues 93-121 / Source method: obtained synthetically / Details: D-amino acids / Source: (synth.) synthetic construct (others) / References: UniProt: P56254, ALL-D KALATA B1
Sequence detailsTHIS IS A CYCLIC PEPTIDE AND DVA29 CORRESPONDS TO UNP RESIDUE VAL92

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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 DQF-COSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.6 mM D-kalata B1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.6 mM / Component: D-kalata B1
Sample conditionsIonic strength: 1 / pH: 3.5 / Pressure: ambient / Temperature: 290 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ARXBrukerARX5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyGoddarddata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Protocol within CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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