[English] 日本語
Yorodumi- PDB-4fbl: LipS and LipT, two metagenome-derived lipolytic enzymes increase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fbl | ||||||
---|---|---|---|---|---|---|---|
Title | LipS and LipT, two metagenome-derived lipolytic enzymes increase the diversity of known lipase and esterase families | ||||||
Components | LipS lipolytic enzyme | ||||||
Keywords | HYDROLASE / thermostable / Structural Genomics / Enzyme Function Initiative / Structural Proteomics in Europe / SPINE / alpha/beta hydrolase / lipase | ||||||
Function / homology | Alpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / SPERMIDINE Function and homology information | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Chow, J. / Krauss, U. / Dall Antonia, Y. / Fersini, F. / Schmeisser, C. / Schmidt, M. / Menyes, I. / Bornscheuer, U. / Lauinger, B. / Bongen, P. ...Chow, J. / Krauss, U. / Dall Antonia, Y. / Fersini, F. / Schmeisser, C. / Schmidt, M. / Menyes, I. / Bornscheuer, U. / Lauinger, B. / Bongen, P. / Pietruszka, J. / Eckstein, M. / Thum, O. / Liese, A. / Mueller-Dieckmann, J. / Jaeger, K.-E. / Kovacic, F. / Streit, W.R. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: Plos One / Year: 2012 Title: The Metagenome-Derived Enzymes LipS and LipT Increase the Diversity of Known Lipases. Authors: Chow, J. / Kovacic, F. / Dall Antonia, Y. / Krauss, U. / Fersini, F. / Schmeisser, C. / Lauinger, B. / Bongen, P. / Pietruszka, J. / Schmidt, M. / Menyes, I. / Bornscheuer, U.T. / Eckstein, ...Authors: Chow, J. / Kovacic, F. / Dall Antonia, Y. / Krauss, U. / Fersini, F. / Schmeisser, C. / Lauinger, B. / Bongen, P. / Pietruszka, J. / Schmidt, M. / Menyes, I. / Bornscheuer, U.T. / Eckstein, M. / Thum, O. / Liese, A. / Mueller-Dieckmann, J. / Jaeger, K.E. / Streit, W.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4fbl.cif.gz | 208.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4fbl.ent.gz | 166.8 KB | Display | PDB format |
PDBx/mmJSON format | 4fbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/4fbl ftp://data.pdbj.org/pub/pdb/validation_reports/fb/4fbl | HTTPS FTP |
---|
-Related structure data
Related structure data | 4fbmC 1tqhS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 30272.713 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: protein identified by using functional metagenomic screenings Source: (gene. exp.) unidentified (others) / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) #2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.38 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 4.5 Details: 0.1 M NaAcetate, 3 M NaCl,0.01 M spermidine, pH 4.5, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2011 Details: Monochromator (horizontally side diffracting Silicon 111 crystal) |
Radiation | Monochromator: horizontally diffracting monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→40.3 Å / Num. all: 90469 / Num. obs: 85910 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.99→2.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / Num. unique all: 13179 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TQH Resolution: 1.99→40.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.687 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.138 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.736 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→40.3 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.988→2.04 Å / Total num. of bins used: 20
|