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- PDB-1p5t: Crystal Structure of Dok1 PTB Domain -

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Basic information

Entry
Database: PDB / ID: 1p5t
TitleCrystal Structure of Dok1 PTB Domain
ComponentsDocking protein 1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / macrophage colony-stimulating factor signaling pathway / RET signaling / negative regulation of MAPK cascade / cell surface receptor protein tyrosine kinase signaling pathway / Ras protein signal transduction / intracellular signal transduction / nucleus / cytosol
Similarity search - Function
Dok1/2/3, PTB domain / : / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain ...Dok1/2/3, PTB domain / : / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsShi, N. / Ye, S. / Liu, Y. / Zhou, W. / Ding, Y. / Lou, Z. / Qiang, B. / Yuan, J. / Rao, Z.
CitationJournal: J.BIOL.CHEM. / Year: 2004
Title: Structural Basis for the Specific Recognition of RET by the Dok1 Phosphotyrosine Binding Domain
Authors: Shi, N. / Ye, S. / Bartlam, M. / Yang, M. / Wu, J. / Liu, Y. / Sun, F. / Han, X. / Peng, X. / Qiang, B. / Yuan, J. / Rao, Z.
History
DepositionApr 28, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Docking protein 1
B: Docking protein 1


Theoretical massNumber of molelcules
Total (without water)28,9342
Polymers28,9342
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-9 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.110, 56.250, 99.790
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 Docking protein 1 / Dok1


Mass: 14467.001 Da / Num. of mol.: 2 / Fragment: Dok1 PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: mdok1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P97465
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
210 mMMES1droppH6.5
350 mM1dropNaCl
410 mMdithiothreitol1drop
528 %(v/v)PEG60001reservoir
60.1 MMES1reservoirpH6.0
710 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9798, 0.9800, 0.9000
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2003
RadiationMonochromator: Melting Silicom +Fuzed Quartz / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.981
30.91
ReflectionResolution: 2.35→40 Å / Num. all: 18607 / Num. obs: 14730 / % possible obs: 79.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.35→2.43 Å / % possible all: 39.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1refinement
HKL-2000data reduction
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2654 1379 RANDOM
Rwork0.2179 --
all0.2226 18607 -
obs0.2226 14730 -
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 0 16 1703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.77704
X-RAY DIFFRACTIONc_bond_d0.013655
X-RAY DIFFRACTIONc_dihedral_angle_d23.91315
X-RAY DIFFRACTIONc_improper_angle_d1.02584
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.78
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.91315
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02584

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