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Yorodumi- PDB-2f18: GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f18 | ||||||
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Title | GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol | ||||||
Components | Alpha-mannosidase II | ||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE FAMILY 38 | ||||||
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 / mannose metabolic process / N-glycan processing / 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 / mannose metabolic process / N-glycan processing / Golgi stack / protein deglycosylation / protein glycosylation / carbohydrate binding / lysosome / Golgi membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Kuntz, D.A. / Rose, D.R. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography. Authors: Englebienne, P. / Fiaux, H. / Kuntz, D.A. / Corbeil, C.R. / Gerber-Lemaire, S. / Rose, D.R. / Moitessier, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f18.cif.gz | 250.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f18.ent.gz | 195.5 KB | Display | PDB format |
PDBx/mmJSON format | 2f18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f18_validation.pdf.gz | 804.4 KB | Display | wwPDB validaton report |
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Full document | 2f18_full_validation.pdf.gz | 820.4 KB | Display | |
Data in XML | 2f18_validation.xml.gz | 50 KB | Display | |
Data in CIF | 2f18_validation.cif.gz | 78.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/2f18 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/2f18 | HTTPS FTP |
-Related structure data
Related structure data | 2f1aC 2f1bC 1hwwS 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: 119701.617 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alpha-Man-II, GmII / Plasmid: pMTBIP_NHIS / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cell References: GenBank: 517481, UniProt: Q24451*PLUS, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 1176 molecules
#3: Chemical | ChemComp-PO4 / |
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#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-GB1 / ( |
#6: Chemical | ChemComp-MPD / ( |
#7: 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: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Tris, PEG 6K, MPD, NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793376 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793376 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 257854 / Num. obs: 257516 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.1 / Num. unique all: 25391 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HWW Resolution: 1.3→29.85 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 536245.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: The data was collected to 1.21, but since the I/sigmaI was not great in the last shell, data was only refined to a 1.3 A stucture. However sf file contains all the data. The difference in ...Details: The data was collected to 1.21, but since the I/sigmaI was not great in the last shell, data was only refined to a 1.3 A stucture. However sf file contains all the data. The difference in unique reflections is a difference in the way good reflections are assessed between scalepack and CNS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.9992 Å2 / ksol: 0.325707 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→29.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.38 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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