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- PDB-1wk1: Solution structure of Lectin C-type domain derived from a hypothe... -

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Basic information

Entry
Database: PDB / ID: 1wk1
TitleSolution structure of Lectin C-type domain derived from a hypothetical protein from C. elegans
ComponentsHypothetical protein yk1067a12
KeywordsSUGAR BINDING PROTEIN / Lectin C-type domain / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


MD domain / : / MD / Laminin-type EGF domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / von Willebrand factor type A domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like ...MD domain / : / MD / Laminin-type EGF domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / von Willebrand factor type A domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Epidermal growth factor-like domain. / von Willebrand factor A-like domain superfamily / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKobayashi, N. / Koshiba, S. / Inoue, M. / Tochio, N. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of Lectin C-type domain derived from a hypothetical protein from C. elegans
Authors: Kobayashi, N. / Koshiba, S. / Inoue, M. / Tochio, N. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yk1067a12


Theoretical massNumber of molelcules
Total (without water)16,4201
Polymers16,4201
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical protein yk1067a12 / wnt inhibitory family member


Mass: 16419.799 Da / Num. of mol.: 1 / Fragment: Lectin C-type homologue domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Description: Cell-free protein synthesis / Gene: NIG Kohara Sugano clone yk1067a12 / Plasmid: P030929-39 / References: UniProt: Q19853

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.89mM Lectin C-type domain U-13C,15N; 20mM Phosphate buffer Na (pH6.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6 / Pressure: ambient / Temperature: 298 K

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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: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.901Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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