+Open data
-Basic information
Entry | Database: PDB / ID: 1hxk | ||||||
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Title | GOLGI ALPHA-MANNOSIDASE II IN COMPLEX WITH DEOXYMANNOJIRIMICIN | ||||||
Components | ALPHA-MANNOSIDASE IIMannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase | ||||||
Keywords | HYDROLASE / N-terminal alpha-beta domain / three helix bundle / 2 C-terminal beta barrels | ||||||
Function / homology | Function and homology information mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack ...mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack / protein deglycosylation / protein glycosylation / carbohydrate binding / Golgi membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | van den Elsen, J.M.H. / Kuntz, D.A. / Rose, D.R. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Structure of Golgi alpha-mannosidase II: a target for inhibition of growth and metastasis of cancer cells. Authors: van den Elsen, J.M. / Kuntz, D.A. / Rose, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hxk.cif.gz | 240.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hxk.ent.gz | 186.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/1hxk ftp://data.pdbj.org/pub/pdb/validation_reports/hx/1hxk | HTTPS FTP |
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-Related structure data
Related structure data | 1htySC 1hwwC 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 116222.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell (production host): S2 / Production host: Drosophila melanogaster (fruit fly) References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 986 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-DMJ / |
#5: Chemical | ChemComp-MRD / ( |
#6: 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: 2.3 Å3/Da / Density % sol: 46.5 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, MPD, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 27, 2000 Details: bent cylindrical Si-mirror (Rh coating) bend cylindrical Ge(111) monochromator |
Radiation | Monochromator: bend cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→85.9 Å / Num. all: 158223 / Num. obs: 148337 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 14.6 Å2 / Limit h max: 42 / Limit h min: 0 / Limit k max: 66 / Limit k min: 0 / Limit l max: 87 / Limit l min: 0 / Observed criterion F max: 591889.39 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.3 / Num. unique all: 9246 / % possible all: 56 |
Reflection | *PLUS Highest resolution: 1.69 Å / Num. obs: 114653 / % possible obs: 97.8 % / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS Highest resolution: 1.69 Å / Lowest resolution: 1.75 Å / % possible obs: 92.6 % / Rmerge(I) obs: 0.186 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HTY Resolution: 1.5→85.9 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 40.8767 Å2 / ksol: 0.371343 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.39 Å2 / Biso mean: 15.87 Å2 / Biso min: 3.31 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→85.9 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: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.69 Å / Lowest resolution: 500 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.1969 / Rfactor Rfree: 0.2156 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.275 / % reflection Rfree: 1.8 % / Rfactor Rwork: 0.256 |