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- PDB-2lr7: Cathelicidin-PY -

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Basic information

Entry
Database: PDB / ID: 2lr7
TitleCathelicidin-PY
ComponentsCathelicidin-PY
KeywordsUNKNOWN FUNCTION
Function / homologyCathelicidin-PY
Function and homology information
Biological speciesRana catesbeiana (American bullfrog)
MethodSOLUTION NMR / distance geometry
Model detailsclosest to the average, model 1
AuthorsYang, J.
CitationJournal: To be Published
Title: Structure of Cathelicidin-PY
Authors: Yang, J. / Wei, L.
History
DepositionMar 27, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathelicidin-PY


Theoretical massNumber of molelcules
Total (without water)3,4341
Polymers3,4341
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Cathelicidin-PY


Mass: 3434.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Production host: Escherichia coli (E. coli) / References: UniProt: M9MMP3*PLUS
Has protein modificationY

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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: 10% mM [U-2H] D2O-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.1 mM / Component: D2O-1 / Isotopic labeling: [U-2H]
Sample conditionsIonic strength: 0.0001 / pH: 6.2 / Pressure: ambient / Temperature: 25 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
NameDeveloperClassification
SparkyGoddardchemical shift assignment
PROCHECKrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 20

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