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Yorodumi- PDB-2rlg: NMR structure of the antimicrobial peptide RP-1 bound to SDS micelles -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rlg | ||||||
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Title | NMR structure of the antimicrobial peptide RP-1 bound to SDS micelles | ||||||
Components | antimicrobial peptide RP-1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / antimicrobial peptide / alpha-helix / amphipathic / micelle | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Bourbigot, S. / Dodd, E. / Horwood, C. / Booth, V. | ||||||
Citation | Journal: Biopolymers / Year: 2009 Title: Antimicrobial peptide RP-1 structure and interactions with anionic versus zwitterionic micelles. Authors: Bourbigot, S. / Dodd, E. / Horwood, C. / Cumby, N. / Fardy, L. / Welch, W.H. / Ramjan, Z. / Sharma, S. / Waring, A.J. / Yeaman, M.R. / Booth, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rlg.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rlg.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rlg_validation.pdf.gz | 332.5 KB | Display | wwPDB validaton report |
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Full document | 2rlg_full_validation.pdf.gz | 393.3 KB | Display | |
Data in XML | 2rlg_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 2rlg_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/2rlg ftp://data.pdbj.org/pub/pdb/validation_reports/rl/2rlg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2170.812 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: solid phase synthesis employing Fmoc (O-fluorenylmethyl-oxycarbonyl) chemistry |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.5mM [U-15N] protein, 0.4mM DSS, 150mM [U-99% 2H] SDS, 0.4mM sodium azide, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | pH: 5 / Pressure: ambient / Temperature: 313 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR constraints | NOE constraints total: 437 / NOE intraresidue total count: 0 / NOE medium range total count: 107 / NOE sequential total count: 140 / Hydrogen bond constraints total count: 22 | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 10 |