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- PDB-2o9s: The second SH3 domain from ponsin -

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Basic information

Entry
Database: PDB / ID: 2o9s
TitleThe second SH3 domain from ponsin
ComponentsPonsin
KeywordsSIGNALING PROTEIN / SH3 DOMAIN / PONSIN
Function / homology
Function and homology information


cell-substrate junction / zonula adherens / flotillin complex / focal adhesion assembly / stress fiber assembly / cell-substrate adhesion / Smooth Muscle Contraction / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process ...cell-substrate junction / zonula adherens / flotillin complex / focal adhesion assembly / stress fiber assembly / cell-substrate adhesion / Smooth Muscle Contraction / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / cytoskeletal protein binding / stress fiber / cell-matrix adhesion / positive regulation of D-glucose import / insulin receptor binding / adherens junction / positive regulation of protein localization to plasma membrane / nuclear matrix / cellular response to insulin stimulus / insulin receptor signaling pathway / signaling receptor complex adaptor activity / actin binding / membrane raft / focal adhesion / centrosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
c-Cbl associated protein, SH3 domain / c-Cbl associated protein, SH3 domain 1 / c-Cbl associated protein, SH3 domain 2 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / : / Variant SH3 domain / Variant SH3 domain ...c-Cbl associated protein, SH3 domain / c-Cbl associated protein, SH3 domain 1 / c-Cbl associated protein, SH3 domain 2 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / : / Variant SH3 domain / Variant SH3 domain / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Sorbin and SH3 domain-containing protein 1 / Sorbin and SH3 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 0.83 Å
AuthorsPinotsis, N. / Wilmanns, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Paxillin and ponsin interact in nascent costameres of muscle cells
Authors: Gehmlich, K. / Pinotsis, N. / Hayess, K. / van der Ven, P.F. / Milting, H. / El Banayosy, A. / Wilmanns, M. / Ehler, E.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ponsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8735
Polymers7,6991
Non-polymers1754
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.743, 36.562, 69.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ponsin


Mass: 7698.707 Da / Num. of mol.: 1 / Fragment: SRC HOMOLOGY 3 (SH3) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORBS1 / Plasmid: PET151 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AED4, UniProt: Q9BX66*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.5M KSCN, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8131 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2006
RadiationMonochromator: Ge SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8131 Å / Relative weight: 1
ReflectionResolution: 0.83→30 Å / Num. all: 60392 / Num. obs: 56189 / % possible obs: 93 % / Redundancy: 7.1 % / Biso Wilson estimate: 4.12 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.7
Reflection shellResolution: 0.83→0.85 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 8.6 / Num. unique all: 3634 / % possible all: 91.5

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: 2O2W

2o2w


Resolution: 0.83→30 Å / Num. parameters: 7073 / Num. restraintsaints: 9649 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1214 1575 2.8 %RANDOM
all0.105 60392 --
obs0.1043 56130 92.7 %-
Refine analyzeNum. disordered residues: 44 / Occupancy sum hydrogen: 539 / Occupancy sum non hydrogen: 677.3
Refinement stepCycle: LAST / Resolution: 0.83→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms605 0 8 173 786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.035
X-RAY DIFFRACTIONs_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.107
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.122
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.058

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