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- PDB-2ltc: Fas1-4, R555W -

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Basic information

Entry
Database: PDB / ID: 2ltc
TitleFas1-4, R555W
ComponentsTransforming growth factor-beta-induced protein ig-h3
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


negative regulation of cell adhesion / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / chondrocyte differentiation / cell adhesion molecule binding / collagen binding / visual perception / extracellular matrix organization / extracellular matrix ...negative regulation of cell adhesion / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / chondrocyte differentiation / cell adhesion molecule binding / collagen binding / visual perception / extracellular matrix organization / extracellular matrix / trans-Golgi network / integrin binding / angiogenesis / collagen-containing extracellular matrix / cell population proliferation / cell adhesion / Amyloid fiber formation / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
FAS1 domain / FAS1 domain / TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / : / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. ...FAS1 domain / FAS1 domain / TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / : / FAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / Roll / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor-beta-induced protein ig-h3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsUnderhaug, J. / Nielsen, N. / Runager, K.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Mutation in transforming growth factor beta induced protein associated with granular corneal dystrophy type 1 reduces the proteolytic susceptibility through local structural stabilization.
Authors: Underhaug, J. / Kolds, H. / Runager, K. / Nielsen, J.T. / Srensen, C.S. / Kristensen, T. / Otzen, D.E. / Karring, H. / Malmendal, A. / Schitt, B. / Enghild, J.J. / Nielsen, N.C.
History
DepositionMay 16, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Nov 27, 2013Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transforming growth factor-beta-induced protein ig-h3


Theoretical massNumber of molelcules
Total (without water)14,4851
Polymers14,4851
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transforming growth factor-beta-induced protein ig-h3 / Beta ig-h3 / Kerato-epithelin / RGD-containing collagen-associated protein / RGD-CAP


Mass: 14484.660 Da / Num. of mol.: 1 / Fragment: Fas1 4 domain / Mutation: R555W, P634A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBI, BIGH3 / Plasmid: pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15582

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D CBCANH
1613D HNCO
1713D HNCA
1813D HN(CA)CO
1913D HN(CO)CA
11013D (H)CCH-TOCSY
11113D 15N-TOCSY-HSQC
11213D 13C-NOESY-HSQC
11313D 15N-NOESY-HSQC
11412D NOESY

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Sample preparation

DetailsContents: 0.2 mM [U-99% 13C; U-99% 15N] FAS1, R555W, 50 mM sodium phosphate, 100 mM sodium chloride, 0.5 mM DSS, 0.5 % sodium azide, 50 mM arginine, 50 mM glutamate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMFAS1-4, R555W-1[U-99% 13C; U-99% 15N]1
50 mMsodium phosphate-21
100 mMsodium chloride-31
0.5 mMDSS-41
0.5 %sodium azide-51
50 mMarginine-61
50 mMglutamate-71
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
REDCATValafar, Homayoun, and James H. Prestegarddata analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1943 / NOE intraresidue total count: 787 / NOE long range total count: 568 / NOE medium range total count: 185 / NOE sequential total count: 403 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 117 / Protein psi angle constraints total count: 117
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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