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- PDB-1vex: F-spondin TSR domain 4 -

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Basic information

Entry
Database: PDB / ID: 1vex
TitleF-spondin TSR domain 4
ComponentsF-spondin
KeywordsCELL ADHESION / F-spondin / TSR
Function / homology
Function and homology information


O-glycosylation of TSR domain-containing proteins / positive regulation of amyloid precursor protein catabolic process / positive regulation of protein processing / LBD domain binding / negative regulation of amyloid-beta formation / extracellular matrix / protein processing / cell adhesion / extracellular region / metal ion binding
Similarity search - Function
Spondin, N-terminal / Spondin, N-terminal domain superfamily / Reeler domain / Spondin_N / Spondin domain profile. / TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / Reeler domain / Reeler domain superfamily / Reelin domain profile. ...Spondin, N-terminal / Spondin, N-terminal domain superfamily / Reeler domain / Spondin_N / Spondin domain profile. / TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Spondin-like TSP1 domain / Spondin-like TSP1 domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPaakkonen, K. / Tossavainen, H. / Permi, P. / Kilpelainen, I. / Guntert, P.
CitationJournal: Proteins / Year: 2006
Title: Solution structures of the first and fourth TSR domains of F-spondin
Authors: Paakkonen, K. / Tossavainen, H. / Permi, P. / Rakkolainen, H. / Rauvala, H. / Raulo, E. / Kilpelainen, I. / Guntert, P.
History
DepositionApr 6, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Dec 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: F-spondin


Theoretical massNumber of molelcules
Total (without water)6,2401
Polymers6,2401
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 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein F-spondin


Mass: 6240.194 Da / Num. of mol.: 1 / Fragment: F-spondin TSR domain 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P35446

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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
131SCT-HMSQC-HA
NMR detailsText: The first two aminoacids (GS) of the sequence come from the expression system and are not part of the native domain sequence

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Sample preparation

DetailsContents: U-13C, U-15N / Solvent system: 20mM bisTris buffer, 95% H2O, 5% D2O
Sample conditionspH: 6.5 / Pressure: AMBIENT / Temperature: 283.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.30Guntert, P. et al.structure solution
OPALp1.3Koradi, R. et al.refinement
NMRPipe2.1Delaglio, F. et alprocessing
Sparky3.1Goddard, T.D. and Kneller, D.G.data analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 848 restraints, 825 are NOE-derived distance constraints, 23 phi angle constraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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