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- PDB-3vzr: Crystal structure of T173S mutant of PhaB from Ralstonia eutropha -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vzr | ||||||
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Title | Crystal structure of T173S mutant of PhaB from Ralstonia eutropha | ||||||
![]() | Acetoacetyl-CoA reductase | ||||||
![]() | OXIDOREDUCTASE / alpha/beta fold | ||||||
Function / homology | ![]() acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ikeda, K. / Tanaka, Y. / Tanaka, I. / Yao, M. | ||||||
![]() | ![]() Title: Directed evolution and structural analysis of NADPH-dependent Acetoacetyl Coenzyme A (Acetoacetyl-CoA) reductase from Ralstonia eutropha reveals two mutations responsible for enhanced kinetics Authors: Matsumoto, K. / Tanaka, Y. / Watanabe, T. / Motohashi, R. / Ikeda, K. / Tobitani, K. / Yao, M. / Tanaka, I. / Taguchi, 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 | ![]() | 100.5 KB | Display | ![]() |
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PDB format | ![]() | 77.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434 KB | Display | ![]() |
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Full document | ![]() | 437.9 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vzpSC ![]() 3vzqC ![]() 3vzsC 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27658.260 Da / Num. of mol.: 2 / Mutation: T173S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.6-1.2M sodium / potassium tartrate, 0.16-0.2M lithium sulfate, 0.1M CHES (pH 8.9-9.9). , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 18, 2010 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 11342 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rsym value: 0.179 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.15 / Num. unique all: 1108 / Rsym value: 0.514 / % possible all: 99.3 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3VZP Resolution: 2.901→19.996 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8569 / SU ML: 0.24 / σ(F): 0 / Phase error: 20.67 / 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 max: 104.16 Å2 / Biso mean: 24.3067 Å2 / Biso min: 6.22 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.901→19.996 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: 4
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