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- PDB-1qk7: Solution structure of Selenocosmia huwena lectin-I(SHL-I) by 2D-NMR -

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Basic information

Entry
Database: PDB / ID: 1qk7
TitleSolution structure of Selenocosmia huwena lectin-I(SHL-I) by 2D-NMR
ComponentsSELENOCOSMIA HUWENA LECTIN-I
KeywordsLECTIN / SELENOCOSMIA HUWENA / SHL-I / CYSTINE KNOT
Function / homologyHuwentoxin, conserved site-1 / Huwentoxin-1 family signature. / Huwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / toxin activity / carbohydrate binding / extracellular region / U5-theraphotoxin-Hs1a 1
Function and homology information
Biological speciesSELENOCOSMIA HUWENA (Chinese earth tiger)
MethodSOLUTION NMR / distance geometry
AuthorsLu, S. / Liang, S. / Gu, X.
Citation
Journal: J.Protein Chem. / Year: 2000
Title: Three Dimensional Structure of Selenocosmia Huwena Lectin-I (Shl-I) from the Venom of the Spider Selenocosmia Huwena by 2D-NMR
Authors: Lu, S. / Liang, S. / Gu, X.
#1: Journal: Toxicon / Year: 1995
Title: A Lectin-Like Peptide Isolated from the Venom of the Chinese Bird Spider Selenocosmia Huwena
Authors: Liang, S. / Pan, X.
History
DepositionJul 10, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SELENOCOSMIA HUWENA LECTIN-I


Theoretical massNumber of molelcules
Total (without water)3,5491
Polymers3,5491
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 / 100STEREOCHEMICAL ENERGY AND THE RESULT OF PROCHECK
RepresentativeModel #8

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Components

#1: Protein/peptide SELENOCOSMIA HUWENA LECTIN-I


Mass: 3549.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SELENOCOSMIA HUWENA (Chinese earth tiger) / Organ: VENOM GLAND / Secretion: VENOM / References: UniProt: Q86C51*PLUS
Compound detailsTHE STRUCTURE OF SHL-I CONSISTS OF A THREE STRANDED ANTI-PARALLEL BETA-SHEET AND THREE TURNS.THE ...THE STRUCTURE OF SHL-I CONSISTS OF A THREE STRANDED ANTI-PARALLEL BETA-SHEET AND THREE TURNS.THE THREE DISULFIDE BRIDGES AND THREE STRANDED ANTI-PARALLEL BETA-SHEET FORM A INHIBITOR CYSTINE KNOT MOTIF.THE C-TERMINAL FRAGMENT FROM LEU28 - TRP32 ADOPTS TWO SET OF CONFORMATIONS CORRESPONDING TO THE CIS(MODELS 11-20) AND TRANS(MODELS 1-10) CONFORMATIONS OF PRO31.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
NMR detailsText: BEST PROCHECK RESULT. NULL

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 20 mM / pH: 4.5 / Pressure: 1 atm / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: distance geometry / Software ordinal: 1 / Details: REQUIRE DIFFERENCES IN THE MODELS
NMR ensembleConformer selection criteria: STEREOCHEMICAL ENERGY AND THE RESULT OF PROCHECK
Conformers calculated total number: 100 / Conformers submitted total number: 20

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