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- PDB-2gto: Oxidized form of ADAP hSH3-N -

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Basic information

Entry
Database: PDB / ID: 2gto
TitleOxidized form of ADAP hSH3-N
ComponentsFYN-binding protein
KeywordsSIGNALING PROTEIN / helically extended SH3 domain (hSH3)
Function / homology
Function and homology information


anchoring junction / Signal regulatory protein family interactions / Generation of second messenger molecules / protein localization to plasma membrane / integrin-mediated signaling pathway / actin cytoskeleton / T cell receptor signaling pathway / immune response / signaling receptor binding / lipid binding ...anchoring junction / Signal regulatory protein family interactions / Generation of second messenger molecules / protein localization to plasma membrane / integrin-mediated signaling pathway / actin cytoskeleton / T cell receptor signaling pathway / immune response / signaling receptor binding / lipid binding / protein-containing complex binding / protein-containing complex / nucleus / plasma membrane / cytosol
Similarity search - Function
Helically-extended SH3 domain / FYB, helically extended SH3 domain / FYN-binding protein 1/2-like / Helically-extended SH3 domain / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Helically-extended SH3 domain / FYB, helically extended SH3 domain / FYN-binding protein 1/2-like / Helically-extended SH3 domain / Variant SH3 domain / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
FYN-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Simulated Annealing with XPLOR NHI, water refinement
AuthorsFreund, C. / Zimmermann, J. / Kuehne, R.
Citation
Journal: Biochemistry / Year: 2007
Title: Redox-Regulated Conformational Changes in an SH3 Domain
Authors: Zimmermann, J. / Kuhne, R. / Sylvester, M. / Freund, C.
#1: Journal: J.Biomol.Nmr / Year: 2005
Title: NMR assignment of the reduced and oxidized forms of the human ADAP hSH3-1 domain.
Authors: Zimmermann, J. / Freund, C.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FYN-binding protein


Theoretical massNumber of molelcules
Total (without water)11,0621
Polymers11,0621
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 / 200closest to average after water refinement
Representative

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Components

#1: Protein FYN-binding protein / ADAP / FYN-T-binding protein / FYB-120/130 / p120/p130 / SLP-76-associated phosphoprotein / SLAP-130


Mass: 11061.803 Da / Num. of mol.: 1 / Fragment: hSH3-N (oxidized)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYB, SLAP130 / Production host: Escherichia coli (E. coli) / References: UniProt: O15117

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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

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Sample preparation

Details
Solution-IDContentsSolvent system
1Uniform (random) labeling with 15N90% H2O/10% D2O
2Uniform (random) labeling with 15N, 13C90% H2O/10% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker, Rheinstettencollection
XwinNMRBruker, Rheinstettenprocessing
AzaraWayne Boucherprocessing
ANSIG3.3Per Kraulisdata analysis
X-PLORBrungerstructure solution
X-PLORBrungerrefinement
RefinementMethod: Simulated Annealing with XPLOR NHI, water refinement
Software ordinal: 1
NMR ensembleConformer selection criteria: closest to average after water refinement
Conformers calculated total number: 200 / Conformers submitted total number: 20

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