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- PDB-3fy5: Dishevelled PDZ domain homodimer -

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Basic information

Entry
Database: PDB / ID: 3fy5
TitleDishevelled PDZ domain homodimer
ComponentsSegment polarity protein dishevelled homolog DVL-2
KeywordsPROTEIN BINDING / PDZ / dishevelled / cell polarity / Cell membrane / Cell projection / Cilium / Cilium biogenesis/degradation / Cytoplasm / Cytoplasmic vesicle / Developmental protein / Gastrulation / Membrane / Nucleus / Phosphoprotein / Wnt signaling pathway
Function / homology
Function and homology information


convergent extension / ciliary basal body organization / convergent extension involved in gastrulation / establishment of planar polarity / syndecan binding / dorsal/ventral axis specification / gastrulation with mouth forming second / activation of GTPase activity / anterior/posterior axis specification / ciliary rootlet ...convergent extension / ciliary basal body organization / convergent extension involved in gastrulation / establishment of planar polarity / syndecan binding / dorsal/ventral axis specification / gastrulation with mouth forming second / activation of GTPase activity / anterior/posterior axis specification / ciliary rootlet / establishment or maintenance of cell polarity / cilium assembly / ephrin receptor signaling pathway / canonical Wnt signaling pathway / ephrin receptor binding / neurogenesis / neural tube closure / cell cortex / cytoplasmic vesicle / protein stabilization / intracellular signal transduction / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Dishevelled-2 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain ...Dishevelled-2 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Segment polarity protein dishevelled homolog DVL-2
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsEarnest, T. / Friedland, N. / Hung, L.-W. / Moon, R.
History
DepositionJan 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segment polarity protein dishevelled homolog DVL-2
B: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)20,2202
Polymers20,2202
Non-polymers00
Water52229
1
A: Segment polarity protein dishevelled homolog DVL-2

A: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)20,2202
Polymers20,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area9700 Å2
MethodPISA
2
B: Segment polarity protein dishevelled homolog DVL-2

B: Segment polarity protein dishevelled homolog DVL-2


Theoretical massNumber of molelcules
Total (without water)20,2202
Polymers20,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area1070 Å2
ΔGint-7 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.198, 96.198, 93.557
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Segment polarity protein dishevelled homolog DVL-2 / Dishevelled-2 / DSH homolog 2 / Xdsh


Mass: 10109.761 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: dsh, dvl2 / Production host: Escherichia coli (E. coli) / References: UniProt: P51142
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.2 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→29.2 Å / Num. all: 9682 / Num. obs: 9682 / % possible obs: 92.52 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.2 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.684 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.277
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29391 503 5.2 %RANDOM
Rwork0.22933 ---
obs0.23241 9179 92.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.712 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 0 29 1293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221277
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.271.9641728
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5665173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.27925.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31715207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.725157
X-RAY DIFFRACTIONr_chiral_restr0.1530.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021943
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1911.5855
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.22321364
X-RAY DIFFRACTIONr_scbond_it3.8163422
X-RAY DIFFRACTIONr_scangle_it5.5284.5364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 33 -
Rwork0.346 641 -
obs--90.84 %

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