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- PDB-2afj: SPRY domain-containing SOCS box protein 2 (SSB-2) -

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Basic information

Entry
Database: PDB / ID: 2afj
TitleSPRY domain-containing SOCS box protein 2 (SSB-2)
Componentsgene rich cluster, C9 gene
KeywordsGENE REGULATION / beta sandwich
Function / homology
Function and homology information


Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-like ligase-substrate adaptor activity / ubiquitin-dependent protein catabolic process / intracellular signal transduction / protein ubiquitination / cytosol
Similarity search - Function
SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain ...SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
SPRY domain-containing SOCS box protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsMasters, S.L. / Yao, S. / Willson, T.A. / Zhang, J.G. / Palmer, K.R. / Smith, B.J. / Babon, J.J. / Nicola, N.A. / Norton, R.S. / Nicholson, S.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: The SPRY domain of SSB-2 adopts a novel fold that presents conserved Par-4-binding residues
Authors: Masters, S.L. / Yao, S. / Willson, T.A. / Zhang, J.G. / Palmer, K.R. / Smith, B.J. / Babon, J.J. / Nicola, N.A. / Norton, R.S. / Nicholson, S.E.
History
DepositionJul 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 3, 2006Provider: 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_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
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: gene rich cluster, C9 gene


Theoretical massNumber of molelcules
Total (without water)24,8921
Polymers24,8921
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 / 194structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein gene rich cluster, C9 gene / SPRY domain-containing SOCS box protein SSB-2


Mass: 24891.842 Da / Num. of mol.: 1 / Fragment: N-terminal domain plus the SPRY domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ssb-2 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O88838

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
131HNHA
1442D NOESY
1512D NOESY
1641H-15N HSQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Constrants for backbone Phi and Psi were also obtained from program TALOS using backbone chemical shifts.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM U-15N10mM sodium phosphate, 50mM sodium chloride, 2mM EDTA, 0.02%(w/w) sodium azide, 95% H2O, 5% D2O
20.6mM U-15N, 13C10mM sodium phosphate, 50mM sodium chloride, 2mM EDTA, 0.02%(w/w) sodium azide, 95% H2O, 5% D2O
31.0mM U-15N, 13C, 50% random 2H10mM sodium phosphate, 50mM sodium chloride, 2mM EDTA, 0.02%(w/w) sodium azide, 95% H2O, 5% D2O
40.4mM U-15N10mM sodium phosphate, 50mM sodium chloride, 2mM EDTA, 0.02%(w/w) sodium azide, 100% D2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker, Biospincollection
XwinNMR3.5Bruker, Biospinprocessing
XEASY1.3Bartels et aldata analysis
CYANA1.0.6Guntert et alstructure solution
X-PLOR2.9.3Schwietersstructure solution
X-PLOR2.9.3Schwietersrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2074, 1738 are non-redundant NOE-derived distance constraints, 260 dihedral angle restraints, 76 distantce restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 194 / Conformers submitted total number: 20

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