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- PDB-2cqw: Solution structure of RSGI RUH-041, a SMB-like domain from mouse cDNA -

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Basic information

Entry
Database: PDB / ID: 2cqw
TitleSolution structure of RSGI RUH-041, a SMB-like domain from mouse cDNA
ComponentsSushi domain containing 2
KeywordsPROTEIN BINDING / somatomedin_B-like domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of cell cycle G1/S phase transition / negative regulation of cell division / plasma membrane
Similarity search - Function
: / Mucin-4-like C8-3 domain / AMOP domain / AMOP domain / AMOP domain profile. / Adhesion-associated domain present in MUC4 and other proteins / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain ...: / Mucin-4-like C8-3 domain / AMOP domain / AMOP domain / AMOP domain profile. / Adhesion-associated domain present in MUC4 and other proteins / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily
Similarity search - Domain/homology
Sushi domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHamada, T. / Hirota, H. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RSGI RUH-041, a SMB-like domain from mouse cDNA
Authors: Hamada, T. / Hirota, H. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sushi domain containing 2


Theoretical massNumber of molelcules
Total (without water)8,3551
Polymers8,3551
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 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Sushi domain containing 2 / RSGI RUH-041 / a somatomedin_B-like domain


Mass: 8355.288 Da / Num. of mol.: 1 / Fragment: SMB-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Susd2 / Plasmid: P040315-19 / References: UniProt: Q9DBX3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: This structure was determined using 3D NMR techniques

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Sample preparation

DetailsContents: 1.06mM SMB-like domain U-15N,13C; 20mM d-Tris-HCl buffer (pH 7.0); 100mM NaCl; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA1.0.8Guntert, P.structure solution
CYANA1.0.8Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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