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- PDB-1udk: Solution Structure of Nawaprin -

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Basic information

Entry
Database: PDB / ID: 1udk
TitleSolution Structure of Nawaprin
ComponentsNawaprin
KeywordsUNKNOWN FUNCTION / antiparallel beta-sheet / spiral backbone configuration
Function / homology
Function and homology information


venom-mediated disruption of cell wall in another organism / peptidase inhibitor activity / defense response to bacterium / extracellular region
Similarity search - Function
Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesNaja nigricollis (spitting cobra)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics
AuthorsTorres, A.M. / Wong, H.Y. / Desai, M. / Moochhala, S. / Kuchel, P.W. / Kini, R.M.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Identification of a Novel Family of Proteins in Snake Venoms: Purification and Structural Characterization of Nawaprin from Naja nigricollis Snake Venom
Authors: Torres, A.M. / Wong, H.Y. / Desai, M. / Moochhala, S. / Kuchel, P.W. / Kini, R.M.
History
DepositionMay 1, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nawaprin


Theoretical massNumber of molelcules
Total (without water)5,3001
Polymers5,3001
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 / 3000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Nawaprin


Mass: 5300.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja nigricollis (spitting cobra) / Secretion: venom / References: UniProt: P60589*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: The structures were determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.7mM Nawaprin / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: no salt added / pH: 3.1 / Pressure: ambient / Temperature: 298 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 spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
XwinNMR3.1Bukerprocessing
XEASY1.3.13Bartels, C., Xia, T., Billeter, M., Guntert, P., Wuthrich, K.data analysis
INFITSzyperski, I., Guntert, P., Otting, G., Wuthrich, K.data analysis
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.structure solution
CNS1.1refinement
RefinementMethod: simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 530 restraints, 503 are NOE-derived distance restraints, 9 dihedral angle restraints, 18 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 20

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