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- PDB-2o2w: Extending powder diffraction to proteins: structure solution of t... -

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Basic information

Entry
Database: PDB / ID: 2o2w
TitleExtending powder diffraction to proteins: structure solution of the second SH3 domain from ponsin
ComponentsPonsin
KeywordsSIGNALING PROTEIN / powder diffraction / SH3 / 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 glycogen biosynthetic process / positive regulation of insulin receptor signaling pathway / 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 glycogen biosynthetic process / positive regulation of insulin receptor signaling pathway / positive regulation of lipid biosynthetic process / stress fiber / cytoskeletal protein binding / cell-matrix adhesion / positive regulation of D-glucose import / adherens junction / positive regulation of protein localization to plasma membrane / insulin receptor binding / 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 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Sorbin and SH3 domain-containing protein 1 / Sorbin and SH3 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodPOWDER DIFFRACTION / SYNCHROTRON / Resolution: 2.27 Å
AuthorsPinotsis, N. / Margiolaki, I.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Second SH3 domain of ponsin solved from powder diffraction
Authors: Margiolaki, I. / Wright, J.P. / Wilmanns, M. / Fitch, A.N. / Pinotsis, N.
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 250 REFINEMENT. PROGRAM : GSAS AUTHORS : LARSON & VON DREELE DATA USED IN REFINEMENT RESOLUTION RANGE ... REFINEMENT. PROGRAM : GSAS AUTHORS : LARSON & VON DREELE DATA USED IN REFINEMENT RESOLUTION RANGE HIGH (ANGSTROMS) : 2.27 RESOLUTION RANGE LOW (ANGSTROMS) : 15.29 POWDER DIFFRACTION DATA. FIT TO DATA USED IN REFINEMENT NUMBER OF POWDER PATTERNS : 4 PROFILE R VALUES (%) : 2.97 2.90 2.91 3.28 WEIGHTED PROFILE R VALUES (%) : 4.24 4.02 3.94 4.44 F**2 R VALUES (%) : 21.78 24.94 28.10 14.50 NUMBER OF POWDER PATTERN POINTS : 9100 10666 6154 4359 NUMBER OF REFLECTIONS : 3317 3348 1865 1719 TOTAL NUMBER OF POWDER POINTS : 30279 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. PROTEIN ATOMS : 544 NUCLEIC ACID ATOMS : NULL HETEROGEN ATOMS : NULL SOLVENT ATOMS : 36 MODEL REFINEMENT. NUMBER OF LEAST-SQUARES PARAMETERS : 1752 NUMBER OF RESTRAINTS : 1980 LEAST-SQUARES MATRIX BAND WIDTH : 5 MARQUARDT COEFFICIENT : 5.86 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. NUMBER. BOND ANGLES (DEG) : 2.49 740 INTERATOMIC DISTANCES (A) :0.010 556 TORSION ANGLE RESTRAINTS (E) : 0.30 205 CHIRAL VOLUMES (A**3) :0.161 72 DISTANCES FROM RESTRAINT PLANES (A) :0.014 439 TORSION PSEUDOPOTENTIAL RESTRAINTS (E) : 2.34 92 ANTI-BUMPING DISTANCE RESTRAINTS (A) :0.025 102 HYDROGEN BOND DISTANCE RESTRAINTS (A) :0.170 77 EXPERIMENTAL DETAILS EXPERIMENT TYPE : X-RAY POWDER DIFFRACTION DATE OF DATA COLLECTION : 13-MAR-2006 TEMPERATURE (KELVIN) : 295 PH : SAMPLE HOLDER : 1.5MM GLASS CAPILLARY NUMBER OF CRYSTALS USED : POLYCRYSTAL SLURRY SYNCHROTRON (Y/N) : Y RADIATION SOURCE : ESRF BEAMLINE : ID31 X-RAY GENERATOR MODEL : NULL MONOCHROMATIC OR LAUE (M/L) : M WAVELENGTH OR RANGE (A) : 0.8012034(76), 1.251209(40), 1.242481(32) MONOCHROMATOR : DOUBLE SI(111) OPTICS : 2MM X 8MM BEAM ANALYZER : SI(111) DETECTOR TYPE : NINE AVALANCHE PHOTODIODE (APD) DETECTOR MANUFACTURER : NULL INTENSITY-INTEGRATION SOFTWARE : NULL DATA SCALING SOFTWARE : ID31SUM SOFTWARE USED: GSAS STARTING MODEL: PDB ENTRY 1W70

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ponsin


Theoretical massNumber of molelcules
Total (without water)7,6991
Polymers7,6991
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: POWDER DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 292 K / Method: small tubes / pH: 7.5
Details: TRIS/HCL 0.025M, NaCl 0.9M, pH 7.5, SMALL TUBES, temperature 292K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.8012034, 1.241209, 1.242481
DetectorType: NINE AVALANCHE PHOTODIODE (APD) DETECTORS / Detector: SCINTILLATOR / Date: Mar 13, 2006 / Details: 2mm x 1mm Beam
RadiationMonochromator: DOUBLE SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.80120341
21.2412091
31.2424811
ReflectionResolution: 2.27→36 Å / Num. obs: 32259 / Observed criterion σ(F): 0

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Processing

Software
NameClassification
MOLREPphasing
GSASrefinement
ID31SUMdata scaling

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