+Open data
-Basic information
Entry | Database: PDB / ID: 3k42 | ||||||
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Title | Crystal structure of sCD-MPR mutant E19Q/K137M pH 7.0 | ||||||
Components | Cation-dependent mannose-6-phosphate receptor | ||||||
Keywords | protein transport / sugar binding protein / transport / lysosome / mannose / receptor / sugar binding / Glycoprotein / Membrane / Phosphoprotein / Transmembrane | ||||||
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 REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Olson, L.J. / Sun, G. / Bohnsack, R.N. / Peterson, F.C. / Dahms, N.M. / Kim, J.J.P. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Intermonomer interactions are essential for lysosomal enzyme binding by the cation-dependent mannose 6-phosphate receptor. Authors: Olson, L.J. / Sun, G. / Bohnsack, R.N. / Peterson, F.C. / 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 | 3k42.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k42.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 3k42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k42_validation.pdf.gz | 495.4 KB | Display | wwPDB validaton report |
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Full document | 3k42_full_validation.pdf.gz | 505.8 KB | Display | |
Data in XML | 3k42_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 3k42_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/3k42 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/3k42 | HTTPS FTP |
-Related structure data
Related structure data | 3k41C 3k43C 1m6pS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17444.611 Da / Num. of mol.: 2 / Fragment: UNP residues 29-182 / Mutation: E19Q, K137M, N31Q, N57Q, N68Q, N87Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: M6PR / Plasmid: pPICZalphaA / Production host: Pichia Pastoris (fungus) / Strain (production host): x-33 / References: UniProt: P11456 #2: Sugar | #3: Chemical | #4: Chemical | ChemComp-SO4 / #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: 3.78 Å3/Da / Density % sol: 67.42 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES pH 7.0, 3M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 23014 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.093 / Χ2: 1.434 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.481 / Num. unique all: 2307 / Χ2: 1.194 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1M6P Resolution: 2.3→36.27 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 47.801 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.93 Å2 / Biso mean: 31.566 Å2 / Biso min: 10.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→36.27 Å
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Refine LS restraints |
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Xplor file |
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