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Yorodumi- PDB-6y0z: X-ray structure of Lactobacillus brevis alcohol dehydrogenase mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y0z | ||||||
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Title | X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant Q126K | ||||||
Components | R-specific alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Nucleotide Binding Oxidoreductase Activity | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | ||||||
Authors | Hermann, J. / Bischoff, D. / Janowski, R. / Niessing, D. / Grob, P. / Hekmat, D. / Weuster-Botz, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Crystals / Year: 2021 Title: Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts Authors: Hermann, J. / Bischoff, D. / Grob, P. / Janowski, R. / Hekmat, D. / Niessing, D. / Zacharias, M. / Weuster-Botz, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y0z.cif.gz | 134.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y0z.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 6y0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/6y0z ftp://data.pdbj.org/pub/pdb/validation_reports/y0/6y0z | HTTPS FTP |
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-Related structure data
Related structure data | 6y10C 6y1cC 7a2bC 6h07S S: Starting model for refinement C: citing same article (ref.) |
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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: 27875.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: radh / Production host: Escherichia coli (E. coli) / References: UniProt: Q84EX5 |
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-Non-polymers , 5 types, 299 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.39 Å3/Da / Density % sol: 48.58 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: Protein solution (10 g/L LbADH , 20 mM HEPES/NaOH pH 7.0, 1 mM MgCl2 and precipitation buffer (1 mM Tris/HCl pH 7.0, 50 mM MgCl2 and 100 g/L PEG 550 MME) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→46.466 Å / Num. obs: 81466 / % possible obs: 98.9 % / Redundancy: 5.07 % / CC1/2: 0.999 / Net I/σ(I): 10.36 |
Reflection shell | Resolution: 1.21→1.28 Å / Redundancy: 4.4 % / Num. unique obs: 12811 / CC1/2: 0.638 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6h07 Resolution: 1.21→35.98 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.116 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.038 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: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.29 Å2 / Biso mean: 16.963 Å2 / Biso min: 8.3 Å2
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Refinement step | Cycle: final / Resolution: 1.21→35.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.21→1.238 Å / Rfactor Rfree error: 0
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