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Yorodumi- PDB-3axb: Structure of a dye-linked L-proline dehydrogenase from the aerobi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3axb | ||||||
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Title | Structure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix | ||||||
Components | Putative oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / dinucleotide-binding fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å | ||||||
Authors | Sakuraba, H. / Ohshima, T. / Satomura, T. / Yoneda, K. / Hara, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal Structure of Novel Dye-linked L-Proline Dehydrogenase from Hyperthermophilic Archaeon Aeropyrum pernix Authors: Sakuraba, H. / Satomura, T. / Kawakami, R. / Kim, K. / Hara, Y. / Yoneda, K. / Ohshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3axb.cif.gz | 100 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3axb.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 3axb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/3axb ftp://data.pdbj.org/pub/pdb/validation_reports/ax/3axb | 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: 49472.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9YCJ0 | ||
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#2: Chemical | ChemComp-PRO / | ||
#3: Chemical | ChemComp-FAD / | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.96 % Description: the number of unique measured reflections for data collection contains Friedel pairs. Mosaicity: 0.228 ° |
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Crystal grow | Temperature: 293 K / Method: sitting drop / pH: 5.6 Details: PEG4000, ammonium acetate, tri-sodium citrate dihydrate, pH 5.6, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97884, 0.97910, 0.96388 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2010 / Details: Rhodium coated silicon single crystal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Redundancy: 7.6 % / Number: 556722 / Rmerge(I) obs: 0.053 / Χ2: 1.06 / D res high: 1.92 Å / D res low: 50 Å / Num. obs: 73092 / % possible obs: 99.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.92→50 Å / Num. obs: 73214 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.92→30.15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.718 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.59 Å2 / Biso mean: 21.877 Å2 / Biso min: 10.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→30.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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