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- PDB-1p3r: Crystal structure of the phosphotyrosin binding domain(PTB) of mo... -

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Basic information

Entry
Database: PDB / ID: 1p3r
TitleCrystal structure of the phosphotyrosin binding domain(PTB) of mouse Disabled 1(Dab1)
ComponentsDisabled homolog 2
KeywordsSIGNALING PROTEIN / PTB
Function / homology
Function and homology information


Formation of annular gap junctions / Gap junction degradation / pinocytosis / positive regulation of clathrin-dependent endocytosis / renal protein absorption / positive regulation of integrin-mediated signaling pathway / AP-2 adaptor complex binding / clathrin coat of coated pit / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis ...Formation of annular gap junctions / Gap junction degradation / pinocytosis / positive regulation of clathrin-dependent endocytosis / renal protein absorption / positive regulation of integrin-mediated signaling pathway / AP-2 adaptor complex binding / clathrin coat of coated pit / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated vesicle membrane / Clathrin-mediated endocytosis / clathrin adaptor activity / endoderm development / myeloid cell differentiation / cargo receptor activity / clathrin binding / hematopoietic stem cell proliferation / positive regulation of receptor recycling / positive regulation of receptor internalization / negative regulation of protein localization to plasma membrane / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / extrinsic apoptotic signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of substrate adhesion-dependent cell spreading / phosphatidylinositol binding / positive regulation of cell adhesion / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of transcription elongation by RNA polymerase II / establishment of localization in cell / positive regulation of JNK cascade / cell morphogenesis / Wnt signaling pathway / endocytosis / integrin binding / protein transport / in utero embryonic development / positive regulation of cell migration / apical plasma membrane / negative regulation of apoptotic process / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / : / Disabled homolog 2-like, sulfatide-binding motifs / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...: / : / Disabled homolog 2-like, sulfatide-binding motifs / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYun, M. / Keshvara, L. / Park, C.G. / Zhang, Y.M. / Dickerson, J.B. / Zheng, J. / Rock, C.O. / Curran, T. / Park, H.W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structures of the Dab homology domains of mouse disabled 1 and 2.
Authors: Yun, M. / Keshvara, L. / Park, C.G. / Zhang, Y.M. / Dickerson, J.B. / Zheng, J. / Rock, C.O. / Curran, T. / Park, H.W.
History
DepositionApr 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disabled homolog 2
B: Disabled homolog 2
C: Disabled homolog 2


Theoretical massNumber of molelcules
Total (without water)54,1283
Polymers54,1283
Non-polymers00
Water5,675315
1
A: Disabled homolog 2


Theoretical massNumber of molelcules
Total (without water)18,0431
Polymers18,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disabled homolog 2


Theoretical massNumber of molelcules
Total (without water)18,0431
Polymers18,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Disabled homolog 2


Theoretical massNumber of molelcules
Total (without water)18,0431
Polymers18,0431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.15, 128.15, 272.3
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Disabled homolog 2 / DOC-2 / Mitogen-responsive phosphoprotein


Mass: 18042.629 Da / Num. of mol.: 3 / Fragment: PTB domain of mouse Disabled 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: DAB2 OR DOC2 / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P98078
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3.97 Å3/Da / Density % sol: 69.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMHEPES1droppH7.5
21 mMdithiothreitol1drop
31 mMEDTA1drop
420 mg/mlprotein1drop
53.5 Msodium formate1reservoir
650 mMHEPES1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.02466 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02466 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 49672 / % possible obs: 97.1 % / Observed criterion σ(I): -1 / Redundancy: 13.5 % / Rsym value: 0.084 / Net I/σ(I): 54.7
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 54.7 % / Num. measured all: 2717217 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / % possible obs: 99.4 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M7E

1m7e


Resolution: 2.1→30 Å / σ(F): 1.5 /
RfactorNum. reflection
Rfree0.246 -
Rwork0.223 -
obs-39909
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 0 315 3803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.313
X-RAY DIFFRACTIONc_dihedral_angle_d24.14
X-RAY DIFFRACTIONc_improper_angle_d0.687
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.14
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.687

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