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- PDB-2lr5: 1H chemical shift assignments for micasin -

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Basic information

Entry
Database: PDB / ID: 2lr5
Title1H chemical shift assignments for micasin
Componentsmicasin
KeywordsANTIMICROBIAL PROTEIN
Biological speciesArthroderma otae (fungus)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsHarvey, P.J. / Craik, D.J. / Zhu, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Dermatophytic defensin with antiinfective potential
Authors: Zhu, S. / Gao, B. / Harvey, P.J. / Craik, D.J.
History
DepositionMar 22, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: micasin


Theoretical massNumber of molelcules
Total (without water)4,0681
Polymers4,0681
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 micasin


Mass: 4067.702 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arthroderma otae (fungus)
Has protein modificationY
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 PROCESSING.

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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
1312D DQF-COSY
1422D 1H-1H TOCSY
1522D 1H-1H NOESY
1622D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM protein-1, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM protein-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.5 mMentity-11
0.5 mMentity-22
Sample conditionspH: 3 / 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
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky2.6Goddardchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 261 / NOE intraresidue total count: 79 / NOE long range total count: 29 / NOE medium range total count: 49 / NOE sequential total count: 93 / Protein chi angle constraints total count: 7 / Protein phi angle constraints total count: 28 / Protein psi angle constraints total count: 19
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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