[English] 日本語
Yorodumi- PDB-7z2u: Wild-type ferulic acid esterase from Lactobacillus buchneri in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z2u | ||||||
---|---|---|---|---|---|---|---|
Title | Wild-type ferulic acid esterase from Lactobacillus buchneri in complex with ferulate | ||||||
Components | Ferulic acid esterase | ||||||
Keywords | HYDROLASE / Ferulic acid esterase / Lactobacillus buchneri / wild type / ligand | ||||||
Function / homology | feruloyl esterase / feruloyl esterase activity / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / aminopeptidase activity / Alpha/Beta hydrolase fold / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / Ferulic acid esterase Function and homology information | ||||||
Biological species | Lentilactobacillus buchneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Mogodiniyai, K.K. / Reichenbach, T. / Kalyani, D.C. / Keskitalo, M.M. / Divne, C. | ||||||
Funding support | Sweden, 1items
| ||||||
Citation | Journal: Front Microbiol / Year: 2022 Title: Crystal structure of the feruloyl esterase from Lentilactobacillus buchneri reveals a novel homodimeric state. Authors: Kasmaei, K.M. / Kalyani, D.C. / Reichenbach, T. / Jimenez-Quero, A. / Vilaplana, F. / Divne, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7z2u.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7z2u.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 7z2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/7z2u ftp://data.pdbj.org/pub/pdb/validation_reports/z2/7z2u | HTTPS FTP |
---|
-Related structure data
Related structure data | 7z2vC 7z2xC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31690.588 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lentilactobacillus buchneri (bacteria) / Gene: faeA / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1 / References: UniProt: D7RU28, feruloyl esterase #2: Chemical | ChemComp-FER / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.77 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Na cacodylate pH 6.5, 0.2M Ca acetate, 18% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.36 Å / Num. obs: 58652 / % possible obs: 99.9 % / Redundancy: 25.1 % / CC1/2: 0.998 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5738 / CC1/2: 0.613 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: L. buchneri FAE Resolution: 1.9→46.356 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.73 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.356 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|