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- PDB-2kvx: Solution structure of kalata B12 -

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Basic information

Entry
Database: PDB / ID: 2kvx
TitleSolution structure of kalata B12
ComponentsKalata-B12
KeywordsPLANT PROTEIN / kalata
Function / homologyCyclotide superfamily / Cyclotide family / defense response / Kalata-B12
Function and homology information
Biological speciesOldenlandia affinis (plant)
MethodSOLUTION NMR / molecular dynamics
AuthorsWang, C.K.
CitationJournal: Biochemistry / Year: 2011
Title: The role of conserved Glu residue on cyclotide stability and activity: a structural and functional study of kalata B12, a naturally occurring Glu to Asp mutant.
Authors: Wang, C.K. / Clark, R.J. / Harvey, P.J. / Rosengren, K.J. / Cemazar, M. / Craik, D.J.
History
DepositionMar 29, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kalata-B12


Theoretical massNumber of molelcules
Total (without water)2,9051
Polymers2,9051
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-B12


Mass: 2905.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Oldenlandia affinis (plant) / References: UniProt: P85130
Has protein modificationY
Sequence detailsTHIS PEPTIDE IS CYCLIC

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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: 0.3 mM protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.3 mM / Component: entity-1
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker ARX / Manufacturer: Bruker / Model: ARX / Field strength: 900 MHz

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Processing

NMR software
NameClassification
CNSgeometry optimization
CNSrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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