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- PDB-1ews: THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE RABBIT KIDNEY DEF... -

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Basic information

Entry
Database: PDB / ID: 1ews
TitleTHE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE RABBIT KIDNEY DEFENSIN, RK-1
ComponentsRK-1 DEFENSIN
KeywordsANTIMICROBIAL PROTEIN / alpha defensin / triple-stranded beta-sheet
Function / homologyRK-1-like defensin / RK-1-like defensin / defense response to bacterium / extracellular region / Corticostatin-related peptide RK-1
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / simulated annealing
AuthorsMcManus, A.M. / Dawson, N.F. / Wade, J.D. / Craik, D.J.
Citation
Journal: Biochemistry / Year: 2000
Title: Three-dimensional structure of RK-1: a novel alpha-defensin peptide.
Authors: McManus, A.M. / Dawson, N.F. / Wade, J.D. / Carrington, L.E. / Winzor, D.J. / Craik, D.J.
#1: Journal: J.PEPT.SCI. / Year: 2000
Title: Chemical Synthesis, Characterization and Activity of RK-1, a Novel Alpha-Defensin-Related Peptide
Authors: Dawson, N.F. / Craik, D.J. / McManus, A.M. / Dashper, S.G. / Reynolds, E.G. / Tregear, G.W. / Otvos, L. / Wade, J.D.
History
DepositionApr 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 20, 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: RK-1 DEFENSIN


Theoretical massNumber of molelcules
Total (without water)3,7121
Polymers3,7121
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)20 / 50structures with acceptable covalent geometry
RepresentativeModel #9lowest energy

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Components

#1: Protein/peptide RK-1 DEFENSIN / ALPHA-DEFISIN


Mass: 3712.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: KIDNEY / References: UniProt: P81655
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
232E-COSY
2422D NOESY
3532D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM RK190% H2O/10% D2O
21.5 mM RK1100% D2O
31.5 mM RK130% CD3CN: 70% H2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13.5ambient 308 K
23.5ambient 308 K
33.5ambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker ARXBrukerARX5001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
X-EASY1.3.7Eccles, Guntert, Billeter, Wuthrichdata analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 509 distance restraints consisting of 498 NOE-derived distance restraints, 11 restraints from hydrogen bonds and 31 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 50 / Conformers submitted total number: 20

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