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- PDB-1n5p: Solution structure of the cathelin-like domain of protegrins (all... -

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Basic information

Entry
Database: PDB / ID: 1n5p
TitleSolution structure of the cathelin-like domain of protegrins (all amide bonds involving proline residues are in trans conformation)
Componentsprotegrins
KeywordsANTIBIOTIC / cathelin-like domain / cathelicidin / proline isomerization / cystatin fold
Function / homology
Function and homology information


lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / 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 / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsYang, Y. / Sanchez, J.F. / Strub, M.P. / Brutscher, B. / Aumelas, A.
CitationJournal: Biochemistry / Year: 2003
Title: NMR Structure of the Cathelin-like domain of the protegrin-3 Precursor
Authors: Yang, Y. / Sanchez, J.F. / Strub, M.P. / Brutscher, B. / Aumelas, A.
History
DepositionNov 7, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: protegrins


Theoretical massNumber of molelcules
Total (without water)11,7361
Polymers11,7361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 60structures with the least restraint violations
Representative

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Components

#1: Protein protegrins / protegrin 1 / protegrin 2 / protegrin 3 / protegrin 4 / protegrin 5


Mass: 11736.211 Da / Num. of mol.: 1 / Fragment: cathelin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P49933
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA,HNCO,CBCA(CO)NH,3D 15N-separated NOESY
222HC(C)H-TOCSY,3D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5-2mM; U-15N, 13C; 50mM phosphate buffer; pH 6.295% H2O/5% D2O
21.5-2mM; U-15N, 13C; 50mM phosphate buffer; pH 6.2100% D2O
Sample conditionsIonic strength: 100mM / pH: 6.2 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Gifa4.4Delsuc, M.A.processing
X-PLOR3.8Rice, L.M., Brunger, A.T.refinement
XwinNMR2collection
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 15

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