+Open data
-Basic information
Entry | Database: PDB / ID: 6fdd | ||||||||||||
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Title | Crystal Structure of the HHD2 Domain of Whirlin | ||||||||||||
Components | Whirlin | ||||||||||||
Keywords | STRUCTURAL PROTEIN / Usher syndrome / scaffold protein / hearing / deafness | ||||||||||||
Function / homology | Function and homology information axon collateral / paranodal junction maintenance / periciliary membrane compartment / USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / photoreceptor connecting cilium ...axon collateral / paranodal junction maintenance / periciliary membrane compartment / USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / sensory perception of light stimulus / cerebellar Purkinje cell layer formation / photoreceptor connecting cilium / stereocilium tip / inner ear receptor cell stereocilium organization / detection of mechanical stimulus involved in sensory perception of sound / stereocilium bundle / stereocilium / apical dendrite / retina homeostasis / auditory receptor cell stereocilium organization / photoreceptor inner segment / ciliary basal body / dendritic shaft / establishment of localization in cell / actin filament / sensory perception of sound / establishment of protein localization / cilium / presynapse / growth cone / postsynapse / neuron projection / protein domain specific binding / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||||||||
Authors | Delhommel, F. / Cordier, F. / Saul, F. / Haouz, A. / Wolff, N. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: FEBS J. / Year: 2018 Title: Structural plasticity of the HHD2 domain of whirlin. Authors: Delhommel, F. / Cordier, F. / Saul, F. / Chataigner, L. / Haouz, A. / Wolff, N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fdd.cif.gz | 115.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fdd.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/6fdd ftp://data.pdbj.org/pub/pdb/validation_reports/fd/6fdd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 9916.566 Da / Num. of mol.: 6 / Fragment: WHIRLIN DOMAIN HHD2 RESIDUES 420-499 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Whrn, Dfnb31, Kiaa1526 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80VW5 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: ammonium sulfate 1.26M cacodylate 0.7M |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97917 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→49.17 Å / Num. obs: 54049 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 27.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.047 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2966 / CC1/2: 0.681 / Rpim(I) all: 0.63 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→47.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.104
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Displacement parameters | Biso mean: 30.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→47.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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