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- PDB-1hr1: Structure of an indolicidin peptide derivative with P-->A substitution -

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Basic information

Entry
Database: PDB / ID: 1hr1
TitleStructure of an indolicidin peptide derivative with P-->A substitution
ComponentsINDOLICIDIN
KeywordsANTIBIOTIC / ANTIMICROBIAL PROTEIN / alpha-helix / cationic antimicrobial peptide
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / defense response to fungus / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / extracellular space
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Cystatin superfamily
Similarity search - Domain/homology
Biological speciesBOS TAURUS (domestic cattle)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsFriedrich, C.L. / Rozek, A. / Patrzykat, A. / Hancock, R.E.W.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Structure and mechanism of action of an indolicidin peptide derivative with improved activity against Gram-positive bacteria
Authors: Friedrich, C.L. / Rozek, A. / Patrzykat, A. / Hancock, R.E.W.
#1: Journal: Biochemistry / Year: 2000
Title: Structure of the bovine antimicrobial peptide indolicidin bound to dodecylphosphocholine and sodium dodecyl sulfate micelles.
Authors: Rozek, A. / Friedrich, C.L. / Hancock, R.E.W.
History
DepositionDec 20, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INDOLICIDIN


Theoretical massNumber of molelcules
Total (without water)1,8301
Polymers1,8301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 20structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide INDOLICIDIN


Mass: 1830.188 Da / Num. of mol.: 1 / Mutation: P3A,P7A,P10A / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OCCURS NATURALLY IN BOS TAURUS. THE SEQUENCE IS NATURALLY AMIDATED AT C-TERMINUS.
Source: (synth.) BOS TAURUS (domestic cattle) / References: UniProt: P33046
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM CP10A; 200mM dodecylphosphocholine / Solvent system: 10 mM phosphate buffer; 90%H2O,10%D2O
Sample conditionsIonic strength: 200mM DPC / pH: 4 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDealglioprocessing
NMRView4.0.3.Johnsondata analysis
DGII97.2MSIstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on 167 (non-redundant) NOE-derived distance restraints, 77 intraresidue and 90 inter-residue restraints. Structures were generated using DGII (MSI) and then refined using XPLOR.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 15

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