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- PDB-1l6o: XENOPUS DISHEVELLED PDZ DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1l6o
TitleXENOPUS DISHEVELLED PDZ DOMAIN
Components
  • Dapper 1
  • Segment polarity protein dishevelled homolog DVL-2
KeywordsGENE REGULATION / dishevelled / Wnt pathway / PDZ / molecular recognition
Function / homology
Function and homology information


convergent extension / convergent extension involved in gastrulation / ciliary basal body organization / establishment of planar polarity / syndecan binding / dorsal/ventral axis specification / activation of GTPase activity / gastrulation with mouth forming second / anterior/posterior axis specification / ciliary rootlet ...convergent extension / convergent extension involved in gastrulation / ciliary basal body organization / establishment of planar polarity / syndecan binding / dorsal/ventral axis specification / activation of GTPase activity / gastrulation with mouth forming second / 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 / Roll / Winged helix DNA-binding domain superfamily / 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 / Resolution: 2.2 Å
AuthorsCheyette, B.N.R. / Waxman, J.S. / Miller, J.R. / Takemaru, K.-I. / Sheldahl, L.C. / Khlebtsova, N. / Fox, E.P. / Earnest, T. / Moon, R.T.
CitationJournal: Dev.Cell / Year: 2002
Title: Dapper, a Dishevelled-associated antagonist of beta-catenin and JNK signaling, is required for notochord formation
Authors: Cheyette, B.N.R. / Waxman, J.S. / Miller, J.R. / Takemaru, K.-I. / Sheldahl, L.C. / Khlebtsova, N. / Fox, E.P. / Earnest, T. / Moon, R.T.
History
DepositionMar 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / 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 / _pdbx_database_remark.text / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999SEQUENCE AUTHOR HAS MODIFIED RESIDUE 251, AN INITIATING METHIONINE, ON CHAINS A, B AND C AS SELENOMETHIONINE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Segment polarity protein dishevelled homolog DVL-2
B: Segment polarity protein dishevelled homolog DVL-2
C: Segment polarity protein dishevelled homolog DVL-2
D: Dapper 1
E: Dapper 1
F: Dapper 1


Theoretical massNumber of molelcules
Total (without water)34,4446
Polymers34,4446
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-45 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.733, 84.734, 123.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 10588.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P51142
#2: Protein/peptide Dapper 1 / Dishevelled interacting antagonist / Dpr1


Mass: 893.123 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence is naturally found in Xenopus laevis (African clawed frog).
References: GenBank: 20147551
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Khlebtsova, N., (2000) Acta Crystallogr., D56, 212.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris1droppH8.
225 mM1dropNaCl
36-8 mg/mlprotein1drop
4100 mMsodium acetate1reservoirpH4.7
51.4 Msodium formate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0000,0.9796,0.9795,0.9686
DetectorType: ADSC QUANTUM 4 / Detector: CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97951
40.96861
ReflectionResolution: 2.2→54.23 Å / Num. obs: 21376

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Processing

Software
NameVersionClassification
CCDSYSdata collection
HKL-2000data reduction
SOLVEphasing
REFMAC5refinement
CCDSYSdata reduction
HKL-2000data scaling
RefinementResolution: 2.2→54.23 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.95 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32316 1127 5 %RANDOM
Rwork0.27691 ---
obs0.27918 21376 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 64.2111 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 0 25 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0730.0222327
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.5971.9773132
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1173298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.40115446
X-RAY DIFFRACTIONr_chiral_restr0.3130.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.021696
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3490.31176
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.5211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3860.342
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
X-RAY DIFFRACTIONr_mcbond_it3.7311.51496
X-RAY DIFFRACTIONr_mcangle_it6.10322411
X-RAY DIFFRACTIONr_scbond_it8.0523831
X-RAY DIFFRACTIONr_scangle_it12.4494.5721
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.566 47
Rwork0.542 1032

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