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- PDB-7me4: Structure of the extracellular WNT-binding module in Drosophila R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7me4 | ||||||
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Title | Structure of the extracellular WNT-binding module in Drosophila Ror2/Nrk | ||||||
![]() | Tyrosine-protein kinase transmembrane receptor Ror2 | ||||||
![]() | SIGNALING PROTEIN / WNT signaling / receptor tyrosine kinases / acylation / growth factor signaling / co-receptor / pseudokinases / ligand / receptor / cancer | ||||||
Function / homology | ![]() photoreceptor cell axon guidance / rhabdomere development / protein tyrosine kinase collagen receptor activity / multicellular organism development / positive regulation of kinase activity / muscle cell cellular homeostasis / plasma membrane => GO:0005886 / cell surface receptor protein tyrosine kinase signaling pathway / collagen binding / transmembrane receptor protein tyrosine kinase activity ...photoreceptor cell axon guidance / rhabdomere development / protein tyrosine kinase collagen receptor activity / multicellular organism development / positive regulation of kinase activity / muscle cell cellular homeostasis / plasma membrane => GO:0005886 / cell surface receptor protein tyrosine kinase signaling pathway / collagen binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein tyrosine kinase activity / receptor complex / protein phosphorylation / signal transduction / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mendrola, J.M. / Shi, F. / Perry, K. / Stayrook, S.E. / Lemmon, M.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: ROR and RYK extracellular region structures suggest that receptor tyrosine kinases have distinct WNT-recognition modes. Authors: Shi, F. / Mendrola, J.M. / Sheetz, J.B. / Wu, N. / Sommer, A. / Speer, K.F. / Noordermeer, J.N. / Kan, Z.Y. / Perry, K. / Englander, S.W. / Stayrook, S.E. / Fradkin, L.G. / Lemmon, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.1 KB | Display | ![]() |
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PDB format | ![]() | 94.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7me5C ![]() 1i71S ![]() 3hklS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 32587.643 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP residues 42-321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9V6K3, receptor protein-tyrosine kinase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-PAM / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.03 % / Description: bar |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 3 mg/ml protein, 50 mM Bis-Tris propane (pH 5.0), 21% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 19, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→59.074 Å / Num. all: 36932 / Num. obs: 36932 / % possible obs: 88.5 % / Redundancy: 2.2 % / Rpim(I) all: 0.036 / Rrim(I) all: 0.059 / Rsym value: 0.046 / Net I/av σ(I): 9.4 / Net I/σ(I): 9.1 / Num. measured all: 81880 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HKL 1I71 Resolution: 1.75→42.5 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.91 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.84 Å2 / Biso mean: 41.7807 Å2 / Biso min: 20.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→42.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 17.4457 Å / Origin y: 33.538 Å / Origin z: -17.8196 Å
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Refinement TLS group |
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