+Open data
-Basic information
Entry | Database: PDB / ID: 6z69 | ||||||
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Title | A novel metagenomic alpha/beta-fold esterase | ||||||
Components | Acetyl esterase/lipase | ||||||
Keywords | HYDROLASE / alpha/beta-fold hydrolase / esterase / metagenome / inhibitor-bound / substrate promiscuity | ||||||
Function / homology | Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / 7-hydroxy-4-methyl-2H-chromen-2-one / N-HEXYLPHOSPHONATE ETHYL ESTER / Acetyl esterase/lipase Function and homology information | ||||||
Biological species | Pseudonocardia thermophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Bollinger, A. / Thies, S. / Hoeppner, A. / Kobus, S. / Jaeger, K.-E. / Smits, S.H.J. | ||||||
Citation | Journal: Febs J. / Year: 2021 Title: Crystal structures of a novel family IV esterase in free and substrate-bound form. Authors: Hoppner, A. / Bollinger, A. / Kobus, S. / Thies, S. / Coscolin, C. / Ferrer, M. / Jaeger, K.E. / Smits, S.H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z69.cif.gz | 173.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z69.ent.gz | 132.8 KB | Display | PDB format |
PDBx/mmJSON format | 6z69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/6z69 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/6z69 | HTTPS FTP |
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-Related structure data
Related structure data | 6z68SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40513.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Gene: SAMN05443637_118146 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M6Y2K1 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.13 Å3/Da / Density % sol: 42.33 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, 30 % (w/v) PEG 4000, 2 mM methyl 4-methylumbelliferyl hexylphosphat |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→43.39 Å / Num. obs: 63348 / % possible obs: 98.93 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.811→1.875 Å / Rmerge(I) obs: 0.555 / Num. unique obs: 6223 / CC1/2: 0.82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z68 Resolution: 1.81→43.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.787 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.78 Å2 / Biso mean: 15.82 Å2 / Biso min: 3.49 Å2
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Refinement step | Cycle: final / Resolution: 1.81→43.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.811→1.858 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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