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Yorodumi- PDB-1e8h: STRUCTURE OF THE H61T MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e8h | ||||||
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Title | STRUCTURE OF THE H61T MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN THE APO FORM COMPLEXED BY ADP | ||||||
Components | VANILLYL-ALCOHOL OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / METHANOL UTILIZATION / PEROXISOME / FLAVOENZYME / OXIDASE / CATALYSIS | ||||||
Function / homology | Function and homology information vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / methanol metabolic process / FAD binding / peroxisome Similarity search - Function | ||||||
Biological species | PENICILLIUM SIMPLICISSIMUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Mattevi, A. / Fraaije, M.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Structural Analysis of Flavinylation in Vanillyl-Alcohol Oxidase Authors: Fraaije, M.W. / Van Der Heuvel, R.H.H. / Van Berkel, W.J.H. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e8h.cif.gz | 226 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e8h.ent.gz | 179.1 KB | Display | PDB format |
PDBx/mmJSON format | 1e8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/1e8h ftp://data.pdbj.org/pub/pdb/validation_reports/e8/1e8h | HTTPS FTP |
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-Related structure data
Related structure data | 1e8fC 1e8gC 1qltS C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.238137, -0.971199, 0.007873), Vector: Details | BIOLOGICAL_UNIT: HOMOOCTAMER | |
-Components
#1: Protein | Mass: 62969.934 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PENICILLIUM SIMPLICISSIMUM (fungus) / Description: FUNGUS / Cellular location: INTRACELLULARGlossary of biology / Organelle: PEROXISOMESPeroxisome / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P56216, aryl-alcohol oxidase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | CATALYZES THE CONVERSION OF VANILLIN ALCOHOL TO VANILLIN, AND A WIDE RANGE OF PHENOLIC COMPOUNDS OF ...CATALYZES THE CONVERSION | |
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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: 2.3 Å3/Da / Density % sol: 45.56 % | |||||||||||||||
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Crystal grow | pH: 4.6 / Details: FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6 | |||||||||||||||
Crystal grow | *PLUS pH: 5.1 / Method: vapor diffusion, hanging drop | |||||||||||||||
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: ESRF / Beamline: ID14-3 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 34320 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.393 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 85638 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QLT Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_plane_restr / Dev ideal: 0.01 |