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Yorodumi- PDB-1vlb: STRUCTURE REFINEMENT OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vlb | |||||||||
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Title | STRUCTURE REFINEMENT OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO GIGAS AT 1.28 A | |||||||||
Components | ALDEHYDE OXIDOREDUCTASE | |||||||||
Keywords | OXIDOREDUCTASE / Aldehyde Oxidoreductase / Desulfovibrio Gigas / iron-sulphur cluster | |||||||||
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: 1.28 Å | |||||||||
Authors | Rebelo, J.M. / Dias, J.M. / Huber, R. / Moura, J.J.G. / Romao, M.J. | |||||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2001 Title: Structure refinement of the aldehyde oxidoreductase from Desulfovibrio gigas (MOP) at 1.28 A Authors: Rebelo, J.M. / Dias, J.M. / Huber, R. / Moura, J.J.G. / Romao, M.J. #1: Journal: Science / Year: 1995 Title: Structure of the Aldehyde Oxido-reductase from Desulfovibrio gigas at 2.25 A Resolution: A Member of the Xanthine Oxidase Protein Family Authors: Romao, M.J. / Archer, M. / Moura, I. / Moura, J.J.G. / LeGall, J. / Engh, R. / Schneider, M. / Hof, P. / Huber, R. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: A structure-based catalytic mechanism for the xanthine oxidase family of molybdenum enzymes Authors: Huber, R. / Hof, P. / Duarte, R.O. / Moura, J.J.G. / Moura, I. / Liu, M.-Y. / LeGall, J. / Hille, R. / Archer, M. / Romao, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vlb.cif.gz | 414.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vlb.ent.gz | 335.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vlb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/1vlb ftp://data.pdbj.org/pub/pdb/validation_reports/vl/1vlb | HTTPS FTP |
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-Related structure data
Related structure data | 1alo 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: 97140.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio gigas (bacteria) / References: UniProt: Q46509, aldehyde oxidase |
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-Non-polymers , 6 types, 1248 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PCD / ( | #5: Chemical | #6: Chemical | #7: 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: 2.4 Å3/Da / Density % sol: 48.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MgCl2, isopropyl alcohol, pH 7.5, VAPOR DIFFUSION, SITTING DROP at 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.0004 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 7, 1998 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0004 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→24.4 Å / Num. all: 233755 / Num. obs: 226751 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.036 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.28→1.33 Å / Redundancy: 2 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.436 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ALO 1alo Resolution: 1.28→24.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Displacement parameters | Biso mean: 24.7 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.1 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.28→24.4 Å
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Refine LS restraints |
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