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Yorodumi- PDB-4tmb: CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tmb | |||||||||||||||
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Title | CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588 | |||||||||||||||
Components | Old yellow enzymeNADPH dehydrogenase | |||||||||||||||
Keywords | FLAVOPROTEIN / TIM BARREL MOTIF / DEHYDROGENASE | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Kluyveromyces marxianus (yeast) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||||||||
Authors | Horita, S. / Kataoka, M. / Kitamura, N. / Nakagawa, T. / Miyakawa, T. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Chembiochem / Year: 2015 Title: An Engineered Old Yellow Enzyme that Enables Efficient Synthesis of (4R,6R)-Actinol in a One-Pot Reduction System Authors: Horita, S. / Kataoka, M. / Kitamura, N. / Nakagawa, T. / Miyakawa, T. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tmb.cif.gz | 618.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tmb.ent.gz | 512.2 KB | Display | PDB format |
PDBx/mmJSON format | 4tmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/4tmb ftp://data.pdbj.org/pub/pdb/validation_reports/tm/4tmb | HTTPS FTP |
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-Related structure data
Related structure data | 4tmcC 1oyaS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45947.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Strain: AKU4588 / Gene: oye / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q6I7B7 #2: Chemical | ChemComp-FMN / #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 25%(V/V) PEG3350, 100MM TRIS-HCL, 200MM AMMONIUM SULFATE, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 148617 / % possible obs: 97.6 % / Redundancy: 3.5 % / Net I/σ(I): 21.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OYA Resolution: 1.8→19.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.713 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 25.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.82 Å
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Refine LS restraints |
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