+Open data
-Basic information
Entry | Database: PDB / ID: 7z2v | ||||||
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Title | Ferulic acid esterase variant S114A from Lactobacillus buchneri | ||||||
Components | Ferulic acid esterase | ||||||
Keywords | HYDROLASE / Ferulic acid esterase / Lactobacillus buchneri / mutant S114 | ||||||
Function / homology | feruloyl esterase / feruloyl esterase activity / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / aminopeptidase activity / Alpha/Beta hydrolase fold / ACETATE ION / Ferulic acid esterase Function and homology information | ||||||
Biological species | Lentilactobacillus buchneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å | ||||||
Authors | Mogodiniyai, K.K. / Reichenbach, T. / Kalyani, D.C. / Keskitalo, M.M. / Divne, C. | ||||||
Funding support | Sweden, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z2v.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z2v.ent.gz | 99.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/7z2v ftp://data.pdbj.org/pub/pdb/validation_reports/z2/7z2v | HTTPS FTP |
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-Related structure data
Related structure data | 7z2uC 7z2xC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31674.588 Da / Num. of mol.: 2 / Mutation: S114A 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-CA / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M sodium cacodylate pH 6.5, 0.2 M calcium acetate, 18% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97629 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→46.41 Å / Num. obs: 130627 / % possible obs: 99.3 % / Redundancy: 22.5 % / Biso Wilson estimate: 19.76 Å2 / CC1/2: 1 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1.45→1.5 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 11811 / CC1/2: 0.526 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: L. buchneri FAE Resolution: 1.45→40.14 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.7 Å2 / Biso mean: 24.1526 Å2 / Biso min: 13.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→40.14 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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