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- PDB-1kkt: Structure of P. citrinum alpha 1,2-mannosidase reveals the basis ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kkt | |||||||||
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Title | Structure of P. citrinum alpha 1,2-mannosidase reveals the basis for differences in specificity of the ER and Golgi Class I enzymes | |||||||||
![]() | Mannosyl-oligosaccharide alpha-1,2-mannosidase | |||||||||
![]() | HYDROLASE / (alpha/alpha)7-barrel | |||||||||
Function / homology | ![]() mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / protein glycosylation / carbohydrate metabolic process / calcium ion binding / endoplasmic reticulum / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Lobsanov, Y.D. / Vallee, F. / Imberty, A. / Yoshida, T. / Yip, P. / Herscovics, A. / Howell, P.L. | |||||||||
![]() | ![]() Title: Structure of Penicillium citrinum alpha 1,2-mannosidase reveals the basis for differences in specificity of the endoplasmic reticulum and Golgi class I enzymes. Authors: Lobsanov, Y.D. / Vallee, F. / Imberty, A. / Yoshida, T. / Yip, P. / Herscovics, A. / Howell, P.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.6 KB | Display | ![]() |
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PDB format | ![]() | 163.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 730.5 KB | Display | ![]() |
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Full document | ![]() | 748.6 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kreC ![]() 1krfC ![]() 1dl2S ![]() 1fm1S S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Details | The biological assembly is a monomer |
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Components
#1: Protein | Mass: 56626.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P31723, mannosyl-oligosaccharide 1,2-alpha-mannosidase #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.78 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 6000, potassium phosphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Feb 26, 2000 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / 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→50 Å / Num. all: 49814 / Num. obs: 49814 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.2→2.25 Å / Num. unique all: 2151 / Rsym value: 0.242 / % possible all: 60.1 |
Reflection | *PLUS Num. obs: 49836 / Num. measured all: 174227 |
Reflection shell | *PLUS % possible obs: 60.1 % / Rmerge(I) obs: 0.243 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1DL2 and 1FM1 Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.193 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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