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- PDB-1sij: Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1sij | ||||||
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Title | Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]- | ||||||
![]() | Aldehyde oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / Aldehyde Oxidoreductase / Xanthine Oxidase family / Arsenite Inhibition | ||||||
Function / homology | ![]() aldehyde dehydrogenase (FAD-independent) / aldehyde dehydrogenase (FAD-independent) activity / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boer, D.R. / Thapper, A. / Brondino, C.D. / Romao, M.J. / Moura, J.J.G. | ||||||
![]() | ![]() Title: X-ray Crystal Structure and EPR Spectra of "Arsenite-Inhibited" Desulfovibriogigas Aldehyde Dehydrogenase: A Member of the Xanthine Oxidase Family Authors: Boer, D.R. / Thapper, A. / Brondino, C.D. / Romao, M.J. / Moura, J.J.G. #1: ![]() Title: Crystal Structure of the Xanthine Oxidase-Related Aldehyde Oxido-Reductase from D. gigas Authors: Romao, M.J. / Archer, M. / Moura, I. / Moura, J.J.G. / LeGall, J. / Engh, R. / Schneider, M. / Hof, P. / Huber, R. #2: ![]() Title: Structure Refinement of the Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP) at 1.28 Ang. Authors: Rebelo, J.M. / Dias, J.M. / Huber, R. / Moura, J.J.G. / Romao, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.8 KB | Display | ![]() |
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PDB format | ![]() | 152.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.5 KB | Display | ![]() |
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Full document | ![]() | 805.6 KB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hlr S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 97140.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: biologically relevant dimer cannot be unequivocally identified in the crystal Source: (natural) ![]() |
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-Non-polymers , 6 types, 423 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PCD.gif)
![](data/chem/img/AST.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PCD.gif)
![](data/chem/img/AST.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PCD / ( | #5: Chemical | ChemComp-AST / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.2 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: isopropanol, magnesium chloride, HEPES, sodium arsenite, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2002 Details: Double crystal, Si(111) or Si(311), monochromator and toroidal mirror |
Radiation | Monochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 40781 / Num. obs: 40781 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1947 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HLR ![]() 1hlr Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.03 / SU ML: 0.148 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.393 / ESU R Free: 0.234
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.805 Å2
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Refine analyze | Luzzati coordinate error obs: 0.254 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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