+Open data
-Basic information
Entry | Database: PDB / ID: 3zdn | ||||||
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Title | D11-C mutant of monoamine oxidase from Aspergillus niger | ||||||
Components | MONOAMINE OXIDASE N | ||||||
Keywords | OXIDOREDUCTASE / FLAVIN DEPENDENT OXIDASE / AMINES | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ASPERGILLUS NIGER (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Frank, A. / Ghislieri, D. / Willies, S. / Turner, N.J. / Grogan, G. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Engineering an Enantioselective Amine Oxidase for the Synthesis of Pharmaceutical Building Blocks and Alkaloid Natural Products. Authors: Ghislieri, D. / Green, A.P. / Pontini, M. / Willies, S.C. / Rowles, I. / Frank, A. / Grogan, G. / Turner, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zdn.cif.gz | 389.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zdn.ent.gz | 315.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/3zdn ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zdn | HTTPS FTP |
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-Related structure data
Related structure data | 2vvmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 55367.062 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P46882, monoamine oxidase #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-FAD / #4: Water | ChemComp-HOH / | Sequence details | MUTATIONS AS LISTED [I246T, N336S, M348K, T384N, D385S, F210E, L213T, M242Q, W430G] | |
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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: 52.8 % / Description: NONE |
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Crystal grow | pH: 7 Details: 22% (W/V) PEG3350, 0.2M NA2SO4, 0.1M BIS-TRIS PROPANE AT PH 7.0 AND 200 MM PROLINE. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→99.26 Å / Num. obs: 96920 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.55→2.63 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VVM Resolution: 2.55→99.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.473 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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: 29.739 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→99.26 Å
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Refine LS restraints |
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