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- PDB-1p0g: Structure of Antimicrobial Peptide, HP (2-20) and its Analogues D... -

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Basic information

Entry
Database: PDB / ID: 1p0g
TitleStructure of Antimicrobial Peptide, HP (2-20) and its Analogues Derived from Helicobacter pylori, as Determined by 1H NMR Spectroscopy
Components19-mer peptide from 50S ribosomal protein L1
KeywordsRIBOSOME / coil-helix-coil
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / defense response to bacterium / translation
Similarity search - Function
Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family
Similarity search - Domain/homology
Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL1
Similarity search - Component
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
AuthorsLee, K.H. / Lee, D.G. / Park, Y.K. / Harm, K.S. / Kim, Y.M.
CitationJournal: To be published
Title: Interactions between antimicrobial peptide, HP(2-20) derived from helicobacter pylori, and membrain studied by nmr spectroscopy
Authors: Lee, K.H. / Lee, D.G. / Park, Y.K. / Harm, K.S. / Kim, Y.M.
History
DepositionApr 10, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 19-mer peptide from 50S ribosomal protein L1


Theoretical massNumber of molelcules
Total (without water)2,3261
Polymers2,3261
Non-polymers00
Water0
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
Representative

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Components

#1: Protein/peptide 19-mer peptide from 50S ribosomal protein L1 / ribosomal protein L1


Mass: 2325.836 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of peptide is naturally found in Helicobacter pylori
References: UniProt: Q9ZK21, UniProt: P56029*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

DetailsContents: 1.5MM PEPTIDE; 150MM SDS-D25 / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6 / Pressure: 1 atm / Temperature: 318 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 400 MHz

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Processing

NMR software
NameVersionClassification
Felix95processing
XwinNMR2.5collection
CNS1.1refinement
RefinementMethod: HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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