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- PDB-1wic: Solution structure of the MSP domain of RIKEN cDNA 6030424E15 -

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Basic information

Entry
Database: PDB / ID: 1wic
TitleSolution structure of the MSP domain of RIKEN cDNA 6030424E15
ComponentsHypothetical Protein RIKEN cDNA 6030424E15
KeywordsStructural genomics / unknown function / beta sandwich fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


endoplasmic reticulum-endosome membrane contact site / organelle membrane contact site / positive regulation of monocyte chemotaxis / positive regulation of neutrophil chemotaxis / plasma membrane => GO:0005886 / Neutrophil degranulation / chemotaxis / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / PapD-like superfamily / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily ...Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / PapD-like superfamily / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Motile sperm domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR
AuthorsEndo, H. / Asakura, K. / Nemoto, N. / Takasugi, K. / Izumie, K. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Solution structure of the MSP domain of RIKEN cDNA 6030424E15
Authors: Endo, H. / Asakura, K. / Nemoto, N. / Takasugi, K. / Izumie, K. / Yoshida, M. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 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_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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: 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 RIKEN cDNA 6030424E15


Theoretical massNumber of molelcules
Total (without water)16,3081
Polymers16,3081
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 RIKEN cDNA 6030424E15


Mass: 16307.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell Free Synthesis / Gene: RIKEN cDNA 6030424E15 / Plasmid: P031215-09 / References: UniProt: Q9CWP6

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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: 0.99mM 13C,15N-labeled protein; 20mM Tris-HCl buffer;100mM NaCl; 1mM d10-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7.0 / 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVARIANcollection
NMRPipe2002045Delaglio, F.processing
NMRVew5.0.4Johonson, B. A.data analysis
KUJIRA0.899Kobasyshi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
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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