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- PDB-3t4u: L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Le... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t4u | ||||||
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Title | L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Leads to Unique Peptide Flip and Increased Activity | ||||||
![]() | Arylesterase | ||||||
![]() | OXIDOREDUCTASE / HYDRLOASE | ||||||
Function / homology | ![]() arylesterase / Oxidoreductases / arylesterase activity / peroxidase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kazlauskas, R.J. / Yin, T. / Purpero, V.M. | ||||||
![]() | ![]() Title: L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Leads to Unique Peptide Flip and Increased Activity Authors: Yin, T. / Kazlauskas, R.J. / Purpero, V.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 360.9 KB | Display | ![]() |
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PDB format | ![]() | 292.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.7 KB | Display | ![]() |
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Full document | ![]() | 503.7 KB | Display | |
Data in XML | ![]() | 71.5 KB | Display | |
Data in CIF | ![]() | 102 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3t52C ![]() 1va4S 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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2 | ![]()
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Unit cell |
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Details | There are two trimers of the enzyme in one asymmetric unit. One trimer is the biological assembly. |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 29993.955 Da / Num. of mol.: 6 / Mutation: L29I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1317 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.39 Å3/Da / Density % sol: 71.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1% PEG 400, 1.65M (NH4)2SO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: May 10, 2008 / Details: mirrors |
Radiation | Monochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 200730 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 3.01 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 2.77 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.9 / Num. unique all: 19582 / % possible all: 97.6 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VA4 Resolution: 2.02→48.23 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2377 / WRfactor Rwork: 0.2063 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8409 / SU B: 2.972 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1333 / SU Rfree: 0.1273 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 3 / ESU R Free: 0.127 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.94 Å2 / Biso mean: 21.1125 Å2 / Biso min: 4.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→48.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.072 Å / Total num. of bins used: 20
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