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- PDB-1qx9: Structure of a cyclic indolicidin peptide derivative with higher ... -

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Basic information

Entry
Database: PDB / ID: 1qx9
TitleStructure of a cyclic indolicidin peptide derivative with higher charge
ComponentsINDOLICIDIN DERIVATIVE
KeywordsANTIMICROBIAL PROTEIN / CYCLIC CATIONIC ANTIMICROBIAL PEPTIDE / BETA TURN
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
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsRozek, A. / Powers, J.P. / Friedrich, C.L. / Hancock, R.E.
Citation
Journal: Biochemistry / Year: 2003
Title: Structure-based design of an indolicidin peptide analogue with increased protease stability
Authors: Rozek, A. / Powers, J.P. / Friedrich, C.L. / Hancock, R.E.
#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
DepositionSep 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _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 16, 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:
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Assembly

Deposited unit
A: INDOLICIDIN DERIVATIVE


Theoretical massNumber of molelcules
Total (without water)2,0901
Polymers2,0901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 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 DERIVATIVE / cycloCP-11


Mass: 2089.620 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically
Details: The sequence occurs naturally in Bos taurus (bovine) neutrophils. The sequence is amidated at the C-terminus
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 cycloCP-11 DODECYLPHOSPHOCHOLINE / Solvent system: aqueous
Sample conditionsIonic strength: 200mM DPC / pH: 4.6 / Pressure: AMBIENT / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
X-PLOR3.851BRUNGERrefinement
NMRPipeyear 2002Delagliostructure solution
NMRView4.0.3.Johnsonstructure solution
DGII97.2Accelrys Inc.structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 157 (NON -REDUNDANT) NOE-DERIVED DISTANCE RESTRAINTS, 65 INTRARESIDUE AND 92 INTER-RESIDUE RESTRAINTS. STRUCTURES WERE GENERATED USING DGII (Accelrys) 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: 10

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