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- PDB-4wcv: Haloalkane dehalogenase DhaA mutant from Rhodococcus rhodochrous ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wcv | ||||||
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Title | Haloalkane dehalogenase DhaA mutant from Rhodococcus rhodochrous (T148L+G171Q+A172V+C176G) | ||||||
![]() | Haloalkane dehalogenase![]() | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Holubeva, T. / Prudnikova, T. / Kuta-Smatanova, I. / Rezacova, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Balancing the stability-activity trade-off by fine-tuning dehalogenase access tunnels Authors: Liskova, V. / Bednar, D. / Prudnikova, T. / Rezacova, P. / Koudelakova, T. / Sebestova, E. / Kuta-Smatanova, I. / Brezovsky, J. / Chaloupkova, R. / Damborsky, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.1 KB | Display | ![]() |
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PDB format | ![]() | 111.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3g9xS S: Starting model for refinement |
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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: 34175.961 Da / Num. of mol.: 1 / Mutation: T148L+G171Q+A172V+C176G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P0A3G3, UniProt: P0A3G2*PLUS, ![]() | ||
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#2: Chemical | ChemComp-CL / ![]() | ||
#3: Chemical | ChemComp-PGE / ![]() | ||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.39 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: sodium acetate trihydrate, ammonium acetate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.69→39.42 Å / Num. all: 30835 / Num. obs: 28416 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.76 |
Reflection shell | Resolution: 1.69→1.73 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 9.16 / % possible all: 87.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3G9X Resolution: 1.69→39.42 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.179 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.459 Å2
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Refinement step | Cycle: 1 / Resolution: 1.69→39.42 Å
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Refine LS restraints |
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