+Open data
-Basic information
Entry | Database: PDB / ID: 1dzn | ||||||
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Title | Asp170Ser mutant of vanillyl-alcohol oxidase | ||||||
Components | VANILLYL-ALCOHOL OXIDASE | ||||||
Keywords | FLAVIN-DEPENDENT OXIDASE ENZYME / FLAVIN-DEPENDENT OXIDASE | ||||||
Function / homology | Function and homology information vanillyl-alcohol oxidase / vanillyl-alcohol oxidase activity / methanol metabolic process / : / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase activity / FAD binding / peroxisome / mitochondrion Similarity search - Function | ||||||
Biological species | PENICILLIUM SIMPLICISSIMUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Van Den heuvel, R.H.H. / Fraaije, M.W. / Van Berkel, W.J.H. / Mattevi, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Asp170 is Crucial for the Redox Properties of Vanillyl-Alcohol Oxidase Authors: Van Den Heuvel, R.H.H. / Fraaije, M.W. / Mattevi, A. / Van Berkel, W.J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dzn.cif.gz | 226.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dzn.ent.gz | 180.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dzn_validation.pdf.gz | 1003.4 KB | Display | wwPDB validaton report |
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Full document | 1dzn_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1dzn_validation.xml.gz | 48.7 KB | Display | |
Data in CIF | 1dzn_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/1dzn ftp://data.pdbj.org/pub/pdb/validation_reports/dz/1dzn | HTTPS FTP |
-Related structure data
Related structure data | 1qltS 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: (0.234677, -0.972073), |
-Components
#1: Protein | Mass: 62920.934 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: LINK BETWEEN HIS422 AND FLAVIN RING / Source: (gene. exp.) PENICILLIUM SIMPLICISSIMUM (fungus) / Cellular location: PEROXISOME / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG2 / References: UniProt: P56216, vanillyl-alcohol oxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | CHAIN A, B ENGINEERED | Sequence details | AT FEW PLACES THE SEQUENCE IS IN CONFLICT WITH THE RELATED ENTRY (1VAO) AS DESCRIBED IN SEQADV | |
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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: 2.6 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.60 | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / 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: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 16730 / % possible obs: 83.7 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.323 / % possible all: 84 |
Reflection | *PLUS Num. measured all: 23315 |
Reflection shell | *PLUS % possible obs: 83.8 % / Rmerge(I) obs: 0.323 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QLT Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.8→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: 0.011 |