[English] 日本語
Yorodumi- PDB-2vao: STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vao | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH ISOEUGENOL | ||||||
Components | VANILLYL-ALCOHOL OXIDASE | ||||||
Keywords | 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 / DENSITY AVERAGING, LEAST SQUARES REFINEMENT / Resolution: 2.8 Å | ||||||
Authors | Mattevi, A. | ||||||
Citation | Journal: Structure / Year: 1997 Title: Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity. Authors: Mattevi, A. / Fraaije, M.W. / Mozzarelli, A. / Olivi, L. / Coda, A. / van Berkel, W.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vao.cif.gz | 225.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vao.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/2vao ftp://data.pdbj.org/pub/pdb/validation_reports/va/2vao | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.23341, -0.97158, 0.03932), Vector: |
-Components
#1: Protein | Mass: 63107.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FUNGUS / Source: (natural) Penicillium simplicissimum (fungus) / Cellular location: INTRACELLULARGlossary of biology / Organelle: PEROXISOMESPeroxisome / References: UniProt: P56216, alcohol oxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 40 % / Description: BINDING STUDIES | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.6 / Details: FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6 | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 23480 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.112 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3 / Rsym value: 0.322 / % possible all: 83.1 |
Reflection | *PLUS Num. measured all: 175968 / Rmerge(I) obs: 0.118 |
Reflection shell | *PLUS % possible obs: 83.1 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DENSITY AVERAGING, LEAST SQUARES REFINEMENT Resolution: 2.8→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5-E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.295 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|