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Open data
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Basic information
Entry | Database: PDB / ID: 1e6f | ||||||
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Title | Human MIR-receptor, repeat 11 | ||||||
![]() | CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | ||||||
![]() | RECEPTOR / MIR-RECEPTOR / IGF-II RECEPTOR / TRANSPORT / GLYCOPROTEIN | ||||||
Function / homology | ![]() Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / D-mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / late endosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / signaling receptor activity / spermatogenesis / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Von Buelow, R. / Rajashankar, K.R. / Dauter, M. / Dauter, Z. / Grimme, S. / Schmidt, B. / Von Figura, K. / Uson, I. | ||||||
![]() | ![]() Title: Locating the Anomalous Scatterer Substructures in Halide and Sulfur Phasing Authors: Uson, I. / Schmidt, B. / Von Buelow, R. / Grimme, S. / Von Figura, K. / Dauter, M. / Rajashankar, K.R. / Dauter, Z. / Sheldrick, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61 KB | Display | ![]() |
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PDB format | ![]() | 48.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.8 KB | Display | ![]() |
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Full document | ![]() | 428.8 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: (0.02057, -0.99979, -0.00014), Vector: |
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Components
#1: Protein | Mass: 15564.672 Da / Num. of mol.: 2 Fragment: IGF-II-BINDING DOMAIN, REPEAT 11, RESIDUES 1508-1650 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Water | ChemComp-HOH / | Compound details | TRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES FROM THE GOLGI COMPLEX AND THE CELL SURFACE TO ...TRANSPORT OF PHOSPHORYL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.7 Details: PRECIPITANT: 0.2 M AMMONIUM ACETATE, 0.1 M CACODYLATE PH 5 28% PEG 4000. PROTEIN SOLUTION: 8 MG/ML IN 10 MM TRIS-HCL PH7.5, 150 MM N VAPOUR DIFFUSION, HANGING DROPS,1:1 RATIO. | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 35 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 288 K / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 / Details: BENT CRYSTALS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9057 Å / Relative weight: 1 |
Reflection | Resolution: 1.753→8 Å / Num. obs: 29383 / % possible obs: 99.1 % / Redundancy: 15 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 40.8 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 9.9 / % possible all: 97.3 |
Reflection | *PLUS Lowest resolution: 8 Å / Redundancy: 8.3 % |
Reflection shell | *PLUS % possible obs: 97.4 % / Rmerge(I) obs: 0.089 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 22 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2050.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.2209 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |