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- PDB-2kya: Solution structure of the leader sequence of the patellamide prec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2kya | ||||||
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Title | Solution structure of the leader sequence of the patellamide precursor peptide, PatE1-34 | ||||||
![]() | Patellamide protein | ||||||
![]() | UNKNOWN FUNCTION / Cyclic peptides / PatE / Patellamides / Prochloron / ribosomal peptide synthetase | ||||||
Function / homology | Microcyclamide/patellamide bacteriocin family, leader peptide / Patellamide protein![]() | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Houssen, W.E. / Wright, S.H. / Kalverda, A.P. / Thompson, G.S. / Kelly, S.M. / Jaspars, M. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150 KB | Display | ![]() |
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PDB format | ![]() | 123.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 360.7 KB | Display | ![]() |
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Full document | ![]() | 379.6 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | 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.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: The Solution Conformation of the Leader Sequence of the Prepropeptide for the microcin-like Patellamide | ||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 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 | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.160 / pH: 5.7 / Pressure: ambient / Temperature: 25 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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Processing
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 14 / Conformers submitted total number: 14 |