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Yorodumi- PDB-2vvm: The structure of MAO-N-D5, a variant of monoamine oxidase from As... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vvm | ||||||
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Title | The structure of MAO-N-D5, a variant of monoamine oxidase from Aspergillus niger. | ||||||
Components | MONOAMINE OXIDASE N | ||||||
Keywords | OXIDOREDUCTASE / MONOAMINE OXIDASE / ASPERGILLUS NIGER / FAD / PEROXISOME / FLAVOPROTEIN / ENANTIOSELECTIVITY / DIRECTED EVOLUTION VARIANT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ASPERGILLUS NIGER (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Atkin, K.E. / Hart, S. / Turkenburg, J.P. / Brzozowski, A.M. / Grogan, G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The Structure of Monoamine Oxidase from Aspergillus Niger Provides a Molecular Context for Improvements in Activity Obtained by Directed Evolution. Authors: Atkin, K.E. / Reiss, R. / Koehler, V. / Bailey, K.R. / Hart, S. / Turkenburg, J.P. / Turner, N.J. / Brzozowski, A.M. / Grogan, G.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vvm.cif.gz | 211.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vvm.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/2vvm ftp://data.pdbj.org/pub/pdb/validation_reports/vv/2vvm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55575.453 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: FLAVIN ADENINE DINUCLEOTIDE COFACTOR / Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 DE3 / References: UniProt: P46882, monoamine oxidase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ILE 246 TO MET ENGINEERED RESIDUE IN CHAIN A, ASN 336 TO SER ...ENGINEERED | Sequence details | SEQUENCE DISCREPANC | |
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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: 3.09 Å3/Da / Density % sol: 60.2 % / Description: DATA ORIGINALLY COLLECTED AS HEAVY ATOM SOAK |
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Crystal grow | pH: 7.5 / Details: 10% PEG 3350, 0.2M PROLINE, 0.1M HEPES PH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 20, 2007 / Details: TORODIAL FOCUSING MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 66613 / % possible obs: 99.8 % / Redundancy: 17.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.8 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SELENOMET STRUCTURE OF MONOAMINE OXIDASE Resolution: 1.85→97.59 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.502 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 32-39 DISORDERED AND OMITTED FROM STRUCTURE. DISORDERED SIDECHAINS SET AS ZERO OCCUPANCY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→97.59 Å
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Refine LS restraints |
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