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Yorodumi- PDB-1dgj: CRYSTAL STRUCTURE OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dgj | ||||||
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Title | CRYSTAL STRUCTURE OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 | ||||||
Components | ALDEHYDE OXIDOREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / BETA HALF-BARREL / FOUR-HELIX BUNDLE / BETA BARREL | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Rebelo, J.M. / Macieira, S. / Dias, J.M. / Huber, R. / Romao, M.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Gene sequence and crystal structure of the aldehyde oxidoreductase from Desulfovibrio desulfuricans ATCC 27774. Authors: Rebelo, J. / Macieira, S. / Dias, J.M. / Huber, R. / Ascenso, C.S. / Rusnak, F. / Moura, J.J. / Moura, I. / 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 | 1dgj.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dgj.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dgj_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 1dgj_full_validation.pdf.gz | 480.9 KB | Display | |
Data in XML | 1dgj_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 1dgj_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/1dgj ftp://data.pdbj.org/pub/pdb/validation_reports/dg/1dgj | HTTPS FTP |
-Related structure data
Related structure data | 1alo |
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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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Details | The biological assembly is a crystallographic dimer. |
-Components
#1: Protein | Mass: 98017.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans (bacteria) / Production host: Bacteria (eubacteria) / References: UniProt: Q9REC4, EC: 1.2.-.- | ||||||
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#2: Chemical | #3: Chemical | ChemComp-2MO / | #4: Chemical | ChemComp-MCN / | #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: 3.2 Å3/Da / Density % sol: 61.54 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: ammonium sulphate, MES, dioxane, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.542 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→24.8 Å / Num. all: 31573 / Num. obs: 190328 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.561 / % possible all: 98 |
Reflection | *PLUS Num. obs: 31573 / Num. measured all: 190328 |
Reflection shell | *PLUS % possible obs: 98 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Resolution: 2.8→24.8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→24.8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 24.8 Å / Num. reflection obs: 30614 / σ(F): 2 / % reflection Rfree: 3 % / Rfactor obs: 0.164 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |