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- PDB-1nkl: NK-LYSIN FROM PIG, NMR, 20 STRUCTURES -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1nkl
TitleNK-LYSIN FROM PIG, NMR, 20 STRUCTURES
ComponentsNK-LYSIN
KeywordsSAPOSIN FOLD / ANTIBACTERIAL PEPTIDE / TUMOUROLYTIC PEPTIDE
Function / homology
Function and homology information


defense response to fungus / lipid metabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Granulysin-like / Saposin-like / NK-Lysin / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like ...Granulysin-like / Saposin-like / NK-Lysin / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Antimicrobial peptide NK-lysin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodSOLUTION NMR / VARIABLE TARGET FUNCTION
AuthorsOtting, G. / Liepinsh, E.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Saposin fold revealed by the NMR structure of NK-lysin.
Authors: Liepinsh, E. / Andersson, M. / Ruysschaert, J.M. / Otting, G.
History
DepositionApr 17, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NK-LYSIN


Theoretical massNumber of molelcules
Total (without water)8,9461
Polymers8,9461
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 / 50LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein NK-LYSIN


Mass: 8945.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACTIVE BY MEMBRANE-BINDING / Source: (natural) Sus scrofa (pig) / Organ: INTESTINE / References: UniProt: Q29075

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY

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Sample preparation

Sample conditionspH: 5.5 / Temperature: 309 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX600BrukerDMX6006001
Varian UNITY750VarianUNITY7507502

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Processing

NMR software
NameDeveloperClassification
OPALLUGINBUHL,GUNTERT,BILLETER,WUTHRICHrefinement
DIANAstructure solution
OPALstructure solution
RefinementMethod: VARIABLE TARGET FUNCTION / Software ordinal: 1
Details: USING DEFAULT PARAMETERS PROVIDED BY THE PROGRAM WITH RESTRAINTS FOR PEPTIDE BOND PLANARITY. PROGRAM DIANA BY GUNTERT, BRAUN, WUTHRICH ALSO WAS USED.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 20

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