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Yorodumi- PDB-1krf: STRUCTURE OF P. CITRINUM ALPHA 1,2-MANNOSIDASE REVEALS THE BASIS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1krf | |||||||||
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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 | |||||||||
Components | Mannosyl-oligosaccharide alpha-1,2-mannosidase | |||||||||
Keywords | HYDROLASE / (ALPHA/ALPHA)7-BARREL | |||||||||
Function / homology | Function and homology information 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 | Penicillium citrinum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Lobsanov, Y.D. / Vallee, F. / Imberty, A. / Yoshida, T. / Yip, P. / Herscovics, A. / Howell, P.L. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1krf.cif.gz | 204.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1krf.ent.gz | 164.5 KB | Display | PDB format |
PDBx/mmJSON format | 1krf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1krf_validation.pdf.gz | 758.2 KB | Display | wwPDB validaton report |
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Full document | 1krf_full_validation.pdf.gz | 777 KB | Display | |
Data in XML | 1krf_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 1krf_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/1krf ftp://data.pdbj.org/pub/pdb/validation_reports/kr/1krf | HTTPS FTP |
-Related structure data
Related structure data | 1kktSC 1kreC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56626.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium citrinum (fungus) / Gene: msdC / Plasmid: pTAPM1 / Production host: Aspergillus oryzae (mold) / Strain (production host): MS2 References: UniProt: P31723, mannosyl-oligosaccharide 1,2-alpha-mannosidase |
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-Sugars , 2 types, 6 molecules
#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 |
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-Non-polymers , 3 types, 200 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 4.60, 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 20, 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: 2.14→50 Å / Num. all: 57692 / Num. obs: 57692 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.91 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.14→2.2 Å / Rsym value: 0.376 / % possible all: 89.3 |
Reflection | *PLUS Redundancy: 3.91 % / Num. measured all: 225764 |
Reflection shell | *PLUS % possible obs: 89.3 % / Rmerge(I) obs: 0.376 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KKT Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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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 % reflection Rfree: 10 % / Rfactor obs: 0.199 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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