[English] 日本語
![](img/lk-miru.gif)
- PDB-1keo: TWISTS AND TURNS OF THE CD-MPR: LIGAND-BOUND VERSUS LIGAND-FREE R... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1keo | ||||||
---|---|---|---|---|---|---|---|
Title | TWISTS AND TURNS OF THE CD-MPR: LIGAND-BOUND VERSUS LIGAND-FREE RECEPTOR | ||||||
![]() | cation-dependent mannose-6-phosphate receptor | ||||||
![]() | SUGAR BINDING PROTEIN / p lectin / receptor / mannose 6-phosphate | ||||||
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 | ![]() ![]() | ||||||
![]() | Olson, L.J. / Zhang, J. / Dahms, N.M. / Kim, J.J. | ||||||
![]() | ![]() Title: Twists and turns of the cation-dependent mannose 6-phosphate receptor. Ligand-bound versus ligand-free receptor Authors: Olson, L.J. / Zhang, J. / Dahms, N.M. / Kim, J.J. #1: ![]() 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.P. #2: ![]() 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.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 71.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 474.9 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17443.580 Da / Num. of mol.: 2 / Fragment: (Residues 29-182) / Mutation: N31Q, N57Q, N68Q, N87Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P11456 #2: Sugar | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG 5000 monomethyl ether, 0.2M ammonium acetate, 0.1M cacodoylate, 150 mM Nacl, 50 mM imidazole (pH=6.5), 10 mM Manganese chloride, 5 mM beta-glycerophosphate, VAPOR DIFFUSION, SITTING ...Details: 25% PEG 5000 monomethyl ether, 0.2M ammonium acetate, 0.1M cacodoylate, 150 mM Nacl, 50 mM imidazole (pH=6.5), 10 mM Manganese chloride, 5 mM beta-glycerophosphate, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 9, 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: 2.2→40 Å / Num. all: 18385 / Num. obs: 18385 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.49 / Num. unique all: 138 / % possible all: 70.5 |
Reflection | *PLUS Num. obs: 11338 / Num. measured all: 83198 |
Reflection shell | *PLUS % possible obs: 70.5 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.6488 Å2 / ksol: 0.353773 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.2 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.215 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 43.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS % reflection Rfree: 8.9 % |