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Yorodumi- PDB-4c7z: Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c7z | ||||||
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Title | Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), activated with sodium dithionite and sodium sulfide | ||||||
Components | ALDEHYDE OXIDOREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / MOLYBDENUM ENZYME / MOP / ACTIVATION / INACTIVATION | ||||||
Function / homology | Function and homology information aldehyde dehydrogenase (FAD-independent) / aldehyde dehydrogenase (FAD-independent) activity / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO GIGAS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Correia, H.D. / Romao, M.J. / Santos-Silva, T. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Kinetic and Structural Studies of Aldehyde Oxidoreductase from Desulfovibrio Gigas Reveal a Dithiolene-Based Chemistry for Enzyme Activation and Inhibition by H2O2. Authors: Marangon, J. / Correia, H.D. / Brondino, C.D. / Moura, J.J.G. / Romao, M.J. / Gonzalez, P.J. / Santos-Silva, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c7z.cif.gz | 378.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c7z.ent.gz | 304.3 KB | Display | PDB format |
PDBx/mmJSON format | 4c7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/4c7z ftp://data.pdbj.org/pub/pdb/validation_reports/c7/4c7z | HTTPS FTP |
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-Related structure data
Related structure data | 4c7yC 4c80C 1vlbS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 97156.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO GIGAS (bacteria) References: UniProt: Q46509, aldehyde dehydrogenase (FAD-independent) |
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-Non-polymers , 8 types, 1252 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IPA / | #5: Chemical | ChemComp-BCT / | #6: Chemical | #7: Chemical | ChemComp-PCD / ( | #8: Chemical | ChemComp-PEO / | #9: 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: 2.47 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: VAPOR DIFFUSION, SITTING DROP, AT 277 K. CRYSTALLIZED USING 30% ISOPROPANOL, 0.2M MGCL2, 0.2M HEPES PH 7.6. |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→21.26 Å / Num. obs: 141097 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VLB Resolution: 1.55→123.99 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.095 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.172 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→123.99 Å
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Refine LS restraints |
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