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- PDB-4jbh: 2.2A resolution structure of cobalt and zinc bound thermostable a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jbh | ||||||
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Title | 2.2A resolution structure of cobalt and zinc bound thermostable alcohol dehydrogenase from Pyrobaculum aerophilum | ||||||
![]() | Alcohol dehydrogenase (Zinc) | ||||||
![]() | OXIDOREDUCTASE / Alcohol dehydrogenase / thermostability / Zinc binding | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lovell, S. / Battaile, K.P. / Vitale, A. / Throne, N. / Hu, X. / Shen, M. / D'Auria, S. / Auld, D.S. | ||||||
![]() | ![]() Title: Physicochemical Characterization of a Thermostable Alcohol Dehydrogenase from Pyrobaculum aerophilum. Authors: Vitale, A. / Thorne, N. / Lovell, S. / Battaile, K.P. / Hu, X. / Shen, M. / D'Auria, S. / Auld, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.7 KB | Display | ![]() |
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PDB format | ![]() | 202.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.3 KB | Display | ![]() |
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Full document | ![]() | 467.2 KB | Display | |
Data in XML | ![]() | 46.6 KB | Display | |
Data in CIF | ![]() | 66.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jbgSC ![]() 4jbiC 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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Components
#1: Protein | Mass: 38688.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827 Gene: PAE2687 / Plasmid: pET28-a / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CO / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 25%(w/v) PEG 1500, PCB Buffer , pH 7.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.60497 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→79.266 Å / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3469 / % possible all: 73.5 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4JBG Resolution: 2.2→49.16 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.08 / Stereochemistry target values: ML Details: Note: Friedel pairs were kept separate during refinement.
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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 max: 97.4 Å2 / Biso mean: 37.9155 Å2 / Biso min: 17.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→49.16 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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