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- PDB-2b5b: A reptilian defensin with anti-bacterial and anti-viral activity -

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Basic information

Entry
Database: PDB / ID: 2b5b
TitleA reptilian defensin with anti-bacterial and anti-viral activity
ComponentsDefensin
KeywordsANTIBIOTIC
Function / homologydefense response to bacterium / extracellular region / Defensin-like turtle egg white protein TEWP
Function and homology information
Biological speciesCaretta caretta (Loggerhead turtle)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, energy minimization, molecular dynamics at constant temperature, time, volume
Model type detailsminimized average
AuthorsChattopadhyay, S. / Sinha, N.K. / Banerjee, S. / Roy, D. / Chattopadhyay, D. / Roy, S.
CitationJournal: Proteins / Year: 2006
Title: Small cationic protein from a marine turtle has beta-defensin-like fold and antibacterial and antiviral activity.
Authors: Chattopadhyay, S. / Sinha, N.K. / Banerjee, S. / Roy, D. / Chattopadhyay, D. / Roy, S.
History
DepositionSep 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin


Theoretical massNumber of molelcules
Total (without water)4,0911
Polymers4,0911
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)10 / 1000target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Defensin


Mass: 4091.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caretta caretta (Loggerhead turtle) / Tissue: egg-white / References: UniProt: P0CAP0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
141TQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 5mM egg-white protein, 0.1M NaCl, pH=4.5, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.1M NaCl / pH: 4.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.2Brukerprocessing
DYANA1.5Peter Guentert & Kurt Wuthrich, Zurich, Switzerlandstructure solution
Discover3refinement
RefinementMethod: simulated annealing, torsion angle dynamics, energy minimization, molecular dynamics at constant temperature, time, volume
Software ordinal: 1
Details: The structures are based on a total of 109 NOE-derived distance restraints, 25 angle restraints, 3 disulphide restraints and 4 restraints from hydrogen bonds
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1000 / Conformers submitted total number: 10

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