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- PDB-3was: Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3was | |||||||||
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Title | Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with Man-Glc+PO4 | |||||||||
![]() | 4-O-beta-D-mannosyl-D-glucose phosphorylase | |||||||||
![]() | TRANSFERASE / 5-bladed beta propeller fold / phosphorylase / mannan biodegradation | |||||||||
Function / homology | ![]() 4-O-beta-D-mannosyl-D-glucose phosphorylase / hexosyltransferase activity / cell wall organization / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nakae, S. / Ito, S. / Higa, M. / Senoura, T. / Wasaki, J. / Hijikata, A. / Shionyu, M. / Ito, S. / Shirai, T. | |||||||||
![]() | ![]() Title: Structure of Novel Enzyme in Mannan Biodegradation Process 4-O-beta-d-Mannosyl-d-Glucose Phosphorylase MGP Authors: Nakae, S. / Ito, S. / Higa, M. / Senoura, T. / Wasaki, J. / Hijikata, A. / Shionyu, M. / Ito, S. / Shirai, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.1 KB | Display | ![]() |
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PDB format | ![]() | 153.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 41.6 KB | Display | |
Data in CIF | ![]() | 67 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3watC ![]() 3wauC ![]() 4kmiC ![]() 1vkdS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43939.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5LH68, 4-O-beta-D-mannosyl-D-glucose phosphorylase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.15 Details: 2.0M ammonium sulfate, 2.0M ammonium diphosphate, pH 5.15, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 126091 / Num. obs: 122485 / % possible obs: 97.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 8.6 Å2 / Rmerge(I) obs: 0.052 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 21.1 / Num. unique all: 12631 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VKD Resolution: 1.5→38.379 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9095 / SU ML: 0.13 / σ(F): 1.98 / Phase error: 16.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.07 Å2 / Biso mean: 12.2273 Å2 / Biso min: 2.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→38.379 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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