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Yorodumi- PDB-3zdr: Structure of the Alcohol dehydrogenase (ADH) domain of a bifuncti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zdr | |||||||||
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Title | Structure of the Alcohol dehydrogenase (ADH) domain of a bifunctional ADHE dehydrogenase from Geobacillus thermoglucosidasius NCIMB 11955 | |||||||||
Components | ALCOHOL DEHYDROGENASE DOMAIN OF THE BIFUNCTIONAL ACETALDEHYDE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / BIFUNCTIONAL ALCOHOL/ALDEHYDE DEHYDROGENASE / BIOETHANOL | |||||||||
Function / homology | Function and homology information acetaldehyde dehydrogenase (acetylating) activity / alcohol metabolic process / carbon utilization / alcohol dehydrogenase (NAD+) activity / metal ion binding Similarity search - Function | |||||||||
Biological species | GEOBACILLUS THERMOGLUCOSIDASIUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.504 Å | |||||||||
Authors | Extance, J. / Crennell, S.J. / Eley, K. / Cripps, R. / Hough, D.W. / Danson, M.J. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure of a Bifunctional Alcohol Dehydrogenase Involved in Bioethanol Generation in Geobacillus Thermoglucosidasius Authors: Extance, J. / Crennell, S.J. / Eley, K. / Cripps, R. / Hough, D.W. / Danson, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zdr.cif.gz | 162.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zdr.ent.gz | 130 KB | Display | PDB format |
PDBx/mmJSON format | 3zdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zdr_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 3zdr_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 3zdr_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 3zdr_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/3zdr ftp://data.pdbj.org/pub/pdb/validation_reports/zd/3zdr | HTTPS FTP |
-Related structure data
Related structure data | 1rrmS 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
#1: Protein | Mass: 48693.152 Da / Num. of mol.: 1 / Fragment: RESIDUES 457-867 Source method: isolated from a genetically manipulated source Details: C-TERMINAL ADH DOMAIN, STARTING AT RESIDUE 459 Source: (gene. exp.) GEOBACILLUS THERMOGLUCOSIDASIUS (bacteria) Strain: TM242 Description: THE NCIMB 11955 STRAIN ENGINEERED BY TMO RENEWABLES LTD TO INCREASE ETHANOL PRODUCTION. Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: F8CW95, acetaldehyde dehydrogenase (acetylating), alcohol dehydrogenase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | NON-PUBLISHED GENOME. THE PROTEIN COMES FROM A DIFFERENT STRAIN OF GEOBACILLU |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 5 Details: 0.1 M SODIUM ACETATE PH 5.0, 0.1 M AMMONIUM SULPHATE, 0.3 M SODIUM FORMATE, 11.5% (V/V) PEG2K MME, AND 3-3.5% (V/V) PGA-LM (30% GLYCEROL CRYOPROTECTANT) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2011 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.29 Å / Num. obs: 13897 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.1 / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RRM Resolution: 2.504→48.294 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 23.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.504→48.294 Å
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Refine LS restraints |
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LS refinement shell |
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