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- PDB-1ivz: Solution structure of the SEA domain from murine hypothetical pro... -

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Basic information

Entry
Database: PDB / ID: 1ivz
TitleSolution structure of the SEA domain from murine hypothetical protein homologous to human mucin 16
Componentshypothetical protein 1110008I14RIK
Keywordsstructural genomics / unknown function / SEA domain / mucin 16 / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of wound healing / negative regulation of interleukin-6 production / negative regulation of epithelial cell proliferation / membrane => GO:0016020 / external side of plasma membrane / extracellular space
Similarity search - Function
SEA domain / Mucin-16 / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsMaeda, T. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16)
Authors: Maeda, T. / Inoue, M. / Koshiba, S. / Yabuki, T. / Aoki, M. / Nunokawa, E. / Seki, E. / Matsuda, T. / Motoda, Y. / Kobayashi, A. / Hiroyasu, F. / Shirouzu, M. / Terada, T. / Hayami, N. / ...Authors: Maeda, T. / Inoue, M. / Koshiba, S. / Yabuki, T. / Aoki, M. / Nunokawa, E. / Seki, E. / Matsuda, T. / Motoda, Y. / Kobayashi, A. / Hiroyasu, F. / Shirouzu, M. / Terada, T. / Hayami, N. / Ishizuka, Y. / Shinya, N. / Tatsuguchi, A. / Yoshida, M. / Hirota, H. / Matsuo, Y. / Tani, K. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 2, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein 1110008I14RIK


Theoretical massNumber of molelcules
Total (without water)14,6681
Polymers14,6681
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein hypothetical protein 1110008I14RIK


Mass: 14668.079 Da / Num. of mol.: 1 / Fragment: SEA domain(residues 67-185)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Plasmid: p011109-16 / References: UniProt: Q9D1H1

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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
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Residues 1-7(GSSGSSG),127-132(SGPSSG) are cloning artifacts.

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Sample preparation

DetailsContents: 1.5mM protein U-15N, 13C; 20mM sodium phosphate buffer; 100mM NaCl; 1mM d-DTT; 0.02% sodium azide, 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6.0 / 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
NMRPipe1.8Delaglioprocessing
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 2533 restraints, 2277 are NOE-derived distance constraints, 178 dihedral angle restraints, 78 distance constraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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