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- PDB-1m6p: EXTRACYTOPLASMIC DOMAIN OF BOVINE CATION-DEPENDENT MANNOSE 6-PHOS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m6p | ||||||
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Title | EXTRACYTOPLASMIC DOMAIN OF BOVINE CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR | ||||||
![]() | CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | ||||||
![]() | RECEPTOR / CATION DEPENDENT MANNOSE 6-PHOSPHATE / P-TYPE LECTIN / TRANSPORT | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Roberts, D.L. / Weix, D.J. / Dahms, N.M. / Kim, J.J.-P. | ||||||
![]() | ![]() Title: Molecular basis of lysosomal 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.6 KB | Display | ![]() |
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PDB format | ![]() | 55.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.7 KB | Display | ![]() |
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Full document | ![]() | 497.3 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Noncrystallographic symmetry (NCS) | NCS domain:
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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.) ![]() ![]() ![]() #2: Chemical | #3: Sugar | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion, sitting drop / pH: 6.6 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 144591 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 20.12 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.077 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.8→1.82 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / Rsym value: 0.43 / % possible all: 72.5 |
Reflection | *PLUS Num. obs: 31187 / Num. measured all: 144591 / Rmerge(I) obs: 0.077 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 19.65 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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