+Open data
-Basic information
Entry | Database: PDB / ID: 1l6o | ||||||
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Title | XENOPUS DISHEVELLED PDZ DOMAIN | ||||||
Components |
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Keywords | GENE REGULATION / dishevelled / Wnt pathway / PDZ / molecular recognition | ||||||
Function / homology | Function and homology information convergent extension / ciliary basal body organization / convergent extension involved in gastrulation / establishment of planar polarity / dorsal/ventral axis specification / syndecan binding / 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 / dorsal/ventral axis specification / syndecan binding / gastrulation with mouth forming second / activation of GTPase activity / anterior/posterior axis specification / ciliary rootlet / establishment or maintenance of cell polarity / cilium assembly / canonical Wnt signaling pathway / ephrin receptor signaling pathway / neurogenesis / ephrin receptor binding / 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 | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
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. | ||||||
Citation | Journal: 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 |
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Remark 999 | SEQUENCE AUTHOR HAS MODIFIED RESIDUE 251, AN INITIATING METHIONINE, ON CHAINS A, B AND C AS SELENOMETHIONINE |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l6o.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l6o.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 1l6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/1l6o ftp://data.pdbj.org/pub/pdb/validation_reports/l6/1l6o | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.66 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Khlebtsova, N., (2000) Acta Crystallogr., D56, 212. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0000,0.9796,0.9795,0.9686 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | |||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.2→54.23 Å / Num. obs: 21376 |
-Processing
Software |
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Refinement | Resolution: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.2111 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→54.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20 /
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