[English] 日本語
Yorodumi- PDB-1m6p: EXTRACYTOPLASMIC DOMAIN OF BOVINE CATION-DEPENDENT MANNOSE 6-PHOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m6p | ||||||
---|---|---|---|---|---|---|---|
Title | EXTRACYTOPLASMIC DOMAIN OF BOVINE CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR | ||||||
Components | CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | ||||||
Keywords | RECEPTOR / CATION DEPENDENT MANNOSE 6-PHOSPHATE / P-TYPE LECTIN / 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 / lysosomal membrane ...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 / lysosomal membrane / protein domain specific binding / Golgi apparatus Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.8 Å | ||||||
Authors | Roberts, D.L. / Weix, D.J. / Dahms, N.M. / Kim, J.J.-P. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1m6p.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1m6p.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 1m6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m6p ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6p | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
|
-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: 5B1-4 / Cell line (production host): 5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P11456 #2: Chemical | #3: Sugar | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.8→10 Å / Rfactor Rfree error: 0.0049 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: 0 / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.65 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|