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- PDB-3k7g: Crystal structure of the Indian Hedgehog N-terminal signalling domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k7g | ||||||
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Title | Crystal structure of the Indian Hedgehog N-terminal signalling domain | ||||||
![]() | Indian hedgehog protein![]() | ||||||
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Function / homology | ![]() vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / embryonic skeletal joint development / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation / embryonic camera-type eye morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np ...vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / embryonic skeletal joint development / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation / embryonic camera-type eye morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / RUNX2 regulates chondrocyte maturation / Ligand-receptor interactions / proteoglycan metabolic process / negative regulation of immature T cell proliferation in thymus / chondrocyte proliferation / negative regulation of T cell differentiation in thymus / retinal pigment epithelium development / positive regulation of T cell differentiation in thymus / epithelial cell-cell adhesion / Activation of SMO / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | He, Y.-X. / Kang, Y. / Zhang, W.J. / Yu, J. / Ma, G. / Zhou, C.-Z. | ||||||
![]() | ![]() Title: Crystal structure of the Indian Hedgehog N-terminal signalling domain Authors: He, Y.-X. / Kang, Y. / Zhang, W.J. / Yu, J. / Ma, G. / Zhou, C.-Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.3 KB | Display | ![]() |
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PDB format | ![]() | 36.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1vhhS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 21115.633 Da / Num. of mol.: 1 / Fragment: Indian hedgehog protein N-product Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-GOL / | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl, pH 8.5, 2.0M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→23.9 Å / Num. obs: 32115 / % possible obs: 99.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 11.73 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 10 / Num. unique all: 4650 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1VHH Resolution: 1.5→21.311 Å / Occupancy max: 1 / Occupancy min: 0.56 / FOM work R set: 0.906 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 16.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.135 Å2 / ksol: 0.427 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.89 Å2 / Biso mean: 13.648 Å2 / Biso min: 4.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→21.311 Å
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Refine LS restraints |
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LS refinement shell |
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