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Yorodumi- PDB-1fo3: CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA1,2-MANNOSIDASE IN COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fo3 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA1,2-MANNOSIDASE IN COMPLEX WITH KIFUNENSINE | ||||||
Components | ALPHA1,2-MANNOSIDASE | ||||||
Keywords | HYDROLASE / alpha-alpha7 barrel | ||||||
Function / homology | Function and homology information mannoprotein catabolic process / protein alpha-1,2-demannosylation / Defective MAN1B1 causes MRT15 / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / protein glycosylation / ERAD pathway / ER Quality Control Compartment (ERQC) ...mannoprotein catabolic process / protein alpha-1,2-demannosylation / Defective MAN1B1 causes MRT15 / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / protein glycosylation / ERAD pathway / ER Quality Control Compartment (ERQC) / extracellular vesicle / cytoplasmic vesicle / Maturation of spike protein / viral protein processing / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å | ||||||
Authors | Vallee, F. / Karaveg, K. / Moremen, K.W. / Herscovics, A. / Howell, P.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Structural basis for catalysis and inhibition of N-glycan processing class I alpha 1,2-mannosidases. Authors: Vallee, F. / Karaveg, K. / Herscovics, A. / Moremen, K.W. / 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 | 1fo3.cif.gz | 110.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fo3.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fo3_validation.pdf.gz | 406.1 KB | Display | wwPDB validaton report |
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Full document | 1fo3_full_validation.pdf.gz | 416 KB | Display | |
Data in XML | 1fo3_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1fo3_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/1fo3 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/1fo3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 52781.914 Da / Num. of mol.: 1 / Fragment: C-TERMINAL CATALYTIC DOMAIN / Mutation: DELETION MUTANT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: Q9UKM7, alpha-mannosidase | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | #4: Chemical | ChemComp-KIF / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.35 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MES, calcium, kifunensine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.05 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 406202 / Num. obs: 406202 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.48 / Num. unique all: 1590 / % possible all: 100 |
Reflection | *PLUS Num. obs: 73653 / Num. measured all: 406202 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Resolution: 1.75→28.56 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 372554.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: none
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.47 Å2 / ksol: 0.382 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→28.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.295 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.288 |