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- PDB-2kya: Solution structure of the leader sequence of the patellamide prec... -

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Basic information

Entry
Database: PDB / ID: 2kya
TitleSolution structure of the leader sequence of the patellamide precursor peptide, PatE1-34
ComponentsPatellamide protein
KeywordsUNKNOWN FUNCTION / Cyclic peptides / PatE / Patellamides / Prochloron / ribosomal peptide synthetase
Function / homologyMicrocyclamide/patellamide bacteriocin family, leader peptide / Protein of unknown function (DUF5837) / Family of unknown function (DUF5837) / Patellamide protein
Function and homology information
Biological speciesProchloron didemni (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHoussen, W.E. / Wright, S.H. / Kalverda, A.P. / Thompson, G.S. / Kelly, S.M. / Jaspars, M.
CitationJournal: Chembiochem / Year: 2010
Title: Solution Structure of the Leader Sequence of the Patellamide Precursor Peptide, PatE(1-34).
Authors: Houssen, W.E. / Wright, S.H. / Kalverda, A.P. / Thompson, G.S. / Kelly, S.M. / Jaspars, M.
History
DepositionMay 21, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_cs
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Patellamide protein


Theoretical massNumber of molelcules
Total (without water)3,7091
Polymers3,7091
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)14 / 14structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Patellamide protein


Mass: 3709.252 Da / Num. of mol.: 1 / Fragment: UNP Residues 1-34 / Source method: obtained synthetically
Details: Synthesized on an Applied Biosystems Pioneer peptide synthesizer and HPLC purified
Source: (synth.) Prochloron didemni (bacteria) / References: UniProt: Q52QJ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The Solution Conformation of the Leader Sequence of the Prepropeptide for the microcin-like Patellamide
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H WCOSY
1212D 1H-1H TOCSY 40ms mix
1312D 1H-1H NOESY 60ms mix
1412D 1H-1H TOCSY 80ms mix
151D 1H-1H NOESY 120ms mix
161D 1H-1H NOESY 200ms mix
171D 1H-1H NOESY 300ms mix

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Sample preparation

DetailsContents: 50 % H2O, 50 % [U-100% 2H] TFE, 100 mM sodium chloride, 20 mM sodium phosphate, 1 mM PatE1-34, trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 %H2O-11
50 %TFE-2[U-100% 2H]1
100 mMsodium chloride-31
20 mMsodium phosphate-41
1 mMPatE1-34-51
Sample conditionsIonic strength: 0.16 / pH: 5.7 / Pressure: ambient / Temperature: 25 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2u3Linge, O'Donoghue and Nilgesstructure solution
ARIA2.2u3Linge, O'Donoghue and Nilgeschemical shift assignment
ccpn_analysis1.15ccpn, cambridgedata analysis
ccpn_analysis1.15ccpn, cambridgechemical shift assignment
ccpn_analysis1.15ccpn, cambridgepeak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipe3.0 Rev 2007.068.09.07Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: aria 2 protocol, no solvent refinement, no full relaxation matrix, network anchoring fro the first 4 of 8 rounds of calculation, cooling phases extended by 4 fold
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 14 / Conformers submitted total number: 14

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