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Yorodumi- PDB-4c7a: Crystal structure of the Smoothened CRD, selenomethionine-labeled -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c7a | ||||||
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Title | Crystal structure of the Smoothened CRD, selenomethionine-labeled | ||||||
Components | SMOOTHENED | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information somatic motor neuron differentiation / caudal fin morphogenesis / endocrine system development / angioblast cell migration from lateral mesoderm to midline / swim bladder development / swim bladder morphogenesis / neural plate pattern specification / epithelial tube formation / Hedgehog 'off' state / : ...somatic motor neuron differentiation / caudal fin morphogenesis / endocrine system development / angioblast cell migration from lateral mesoderm to midline / swim bladder development / swim bladder morphogenesis / neural plate pattern specification / epithelial tube formation / Hedgehog 'off' state / : / : / neural plate morphogenesis / otolith morphogenesis / floor plate formation / muscle cell fate commitment / semicircular canal morphogenesis / spinal cord motor neuron cell fate specification / diencephalon development / habenula development / forebrain dorsal/ventral pattern formation / arterial endothelial cell fate commitment / striated muscle cell development / cardioblast differentiation / glial cell development / adenohypophysis development / embryonic neurocranium morphogenesis / dorsal aorta morphogenesis / embryonic viscerocranium morphogenesis / myofibril assembly / embryonic camera-type eye development / cardiac ventricle development / endocardial cell differentiation / spinal cord motor neuron differentiation / patched binding / telencephalon development / embryonic digestive tract morphogenesis / somite development / hindbrain development / neuron fate commitment / cerebellum morphogenesis / endocrine pancreas development / oligodendrocyte development / smooth muscle tissue development / pattern specification process / embryonic pattern specification / exocrine pancreas development / commissural neuron axon guidance / oxysterol binding / positive regulation of smoothened signaling pathway / neural crest cell differentiation / pancreas development / retinal ganglion cell axon guidance / cartilage development / muscle organ development / anterior/posterior pattern specification / inner ear morphogenesis / smoothened signaling pathway / receptor clustering / heart looping / protein kinase A catalytic subunit binding / inner ear development / vasculogenesis / skeletal muscle fiber development / forebrain development / protein sequestering activity / negative regulation of protein phosphorylation / central nervous system development / G protein-coupled receptor activity / axon guidance / cilium / neuron differentiation / retina development in camera-type eye / nervous system development / dendrite / plasma membrane Similarity search - Function | ||||||
Biological species | DANIO RERIO (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Nachtergaele, S. / Whalen, D.M. / Mydock, L.K. / Zhao, Z. / Malinauskas, T. / Krishnan, K. / Ingham, P.W. / Covey, D.F. / Rohatgi, R. / Siebold, C. | ||||||
Citation | Journal: Elife / Year: 2013 Title: Structure and Function of the Smoothened Extracellular Domain in Vertebrate Hedgehog Signaling Authors: Nachtergaele, S. / Whalen, D.M. / Mydock, L.K. / Zhao, Z. / Malinauskas, T. / Krishnan, K. / Ingham, P.W. / Covey, D.F. / Siebold, C. / Rohatgi, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c7a.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c7a.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 4c7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/4c7a ftp://data.pdbj.org/pub/pdb/validation_reports/c7/4c7a | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.1554, 0.9274, 0.3402), Vector: |
-Components
#1: Protein | Mass: 22331.754 Da / Num. of mol.: 2 / Fragment: CYSTEINE-RICH DOMAIN (CRD), RESIDUES 28-210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q90X26 #2: Chemical | ChemComp-ZN / | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | CONSTRUCT CONTAINS ADDITIONAL | |
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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: 2.03 Å3/Da / Density % sol: 38.86 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 100 MM HEPES PH7.0, PEG 6000 20%, 10 MM ZNCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48 Å / Num. obs: 10085 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 26.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 23.7 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 3.9 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.3→30.47 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / SU B: 22.17 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.533 / ESU R Free: 0.296 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.727 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30.47 Å
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