[English] 日本語
Yorodumi- PDB-3t4u: L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Le... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t4u | ||||||
---|---|---|---|---|---|---|---|
Title | L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Leads to Unique Peptide Flip and Increased Activity | ||||||
Components | Arylesterase | ||||||
Keywords | OXIDOREDUCTASE / HYDRLOASE | ||||||
Function / homology | Function and homology information arylesterase / Oxidoreductases / peroxidase activity / arylesterase activity Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å | ||||||
Authors | Kazlauskas, R.J. / Yin, T. / Purpero, V.M. | ||||||
Citation | Journal: To be Published 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3t4u.cif.gz | 360.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3t4u.ent.gz | 292.9 KB | Display | PDB format |
PDBx/mmJSON format | 3t4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/3t4u ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t4u | HTTPS FTP |
---|
-Related structure data
Related structure data | 3t52C 1va4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | There are two trimers of the enzyme in one asymmetric unit. One trimer is the biological assembly. |
-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.) Pseudomonas fluorescens (bacteria) / Plasmid: pL29I / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5alpha / References: UniProt: P22862, arylesterase, Oxidoreductases |
---|
-Non-polymers , 5 types, 1317 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.39 Å3/Da / Density % sol: 71.98 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.98 Å |
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: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→48.23 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.02→2.072 Å / Total num. of bins used: 20
|