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- PDB-2xaa: Alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541 at... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xaa | ||||||
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Title | Alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541 at pH 8.5 in complex with NAD and butane-1,4-diol | ||||||
![]() | SECONDARY ALCOHOL DEHYDROGENASE | ||||||
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Function / homology | ![]() alcohol dehydrogenase (NAD+) activity / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kroutil, W. / Gruber, K. / Grogan, G. | ||||||
![]() | ![]() Title: Structural Insights Into Substrate Specificity and Solvent Tolerance in Alcohol Dehydrogenase Adh-'A' from Rhodococcus Ruber Dsm 44541. Authors: Karabec, M. / Lyskowski, A. / Tauber, K.C. / Steinkellner, G. / Kroutil, W. / Grogan, G. / Gruber, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.3 KB | Display | ![]() |
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PDB format | ![]() | 206 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3jv7SC S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 1 - 345 / Label seq-ID: 1 - 345
NCS oper:
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Components
#1: Protein | Mass: 35221.113 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / ![]() #3: Chemical | ChemComp-ZN / #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow![]() | pH: 8.5 Details: 100 MM BISTRIS PROPANE BUFFER PH 8.5, 20% (W/V) PEG MW 4000, 5 MM CDCL2, 6% V/V 2-PROPANOL, 5% (V/V) 1, 4-BUTANEDIOL. PROTEIN AT 10 MG/ML |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→109.5 Å / Num. obs: 34356 / % possible obs: 9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 87.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3JV7 Resolution: 2.8→109.15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / SU B: 15.282 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→109.15 Å
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Refine LS restraints |
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