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Yorodumi- PDB-1c39: STRUCTURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c39 | |||||||||
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Title | STRUCTURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND TO PENTAMANNOSYL PHOSPHATE | |||||||||
Components | CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | |||||||||
Keywords | SIGNALING PROTEIN / RECEPTOR / CATION DEPENDENT MANNOSE 6-PHOSPHATE / P-TYPE LECT TRANSPORT | |||||||||
Function / homology | Function and homology information Retrograde transport at the Trans-Golgi-Network / Glycosphingolipid catabolism / Lysosome Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / protein targeting to lysosome / Clathrin-mediated endocytosis / lysosomal transport / trans-Golgi network / endosome / protein domain specific binding ...Retrograde transport at the Trans-Golgi-Network / Glycosphingolipid catabolism / Lysosome Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / protein targeting to lysosome / Clathrin-mediated endocytosis / lysosomal transport / trans-Golgi network / endosome / protein domain specific binding / lysosomal membrane / Golgi apparatus Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMEN / Resolution: 1.85 Å | |||||||||
Authors | Olson, L.J. / Zhang, J. / Lee, Y.C. / Dahms, N.M. / Kim, J.J.-P. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Structural basis for recognition of phosphorylated high mannose oligosaccharides by the cation-dependent mannose 6-phosphate receptor. Authors: Olson, L.J. / Zhang, J. / Lee, Y.C. / Dahms, N.M. / Kim, J.J. #1: Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Molecular Basis of Lysosomal Enzyme Recognition:Enzyme Recognition: Three- Dimensional Structure of the Cation-Dependent Mannose 6-Phosphate Receptor Authors: Roberts, D.L. / Weix, D.J. / Dahms, N.M. / Kim, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c39.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c39.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1c39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c39_validation.pdf.gz | 630.2 KB | Display | wwPDB validaton report |
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Full document | 1c39_full_validation.pdf.gz | 635.7 KB | Display | |
Data in XML | 1c39_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1c39_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/1c39 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/1c39 | HTTPS FTP |
-Related structure data
Related structure data | 1m6pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17213.363 Da / Num. of mol.: 2 / Fragment: EXTRACYTOPLASMIC DOMAIN / Mutation: N31Q, N57Q, N68Q, N87Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): 5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P11456 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | #5: 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: 2.7 Å3/Da / Density % sol: 54.4 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.4 / Details: pH 6.40 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 10, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. obs: 48273 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.292 / % possible all: 62.3 |
Reflection | *PLUS Num. obs: 28822 / Num. measured all: 48273 |
Reflection shell | *PLUS % possible obs: 62.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMEN Starting model: PDB ENTRY 1M6P Resolution: 1.85→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 146959.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: SIMULATED ANNEALING
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Displacement parameters | Biso mean: 29.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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