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Yorodumi- PDB-6sya: STRUCTURE OF S192A-ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sya | ||||||
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Title | STRUCTURE OF S192A-ESTER-HYDROLASE EH3 FROM THE METAGENOME OF MARINE SEDIMENTS AT MILAZZO HARBOR (SICILY, ITALY) COMPLEXED WITH METHYL (2R)-2-PHENYLPROPANOATE | ||||||
Components | Esterase | ||||||
Keywords | HYDROLASE / Ester hydrolase / complex | ||||||
Function / homology | Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / triglyceride lipase activity / Alpha/Beta hydrolase fold / methyl (2~{R})-2-phenylpropanoate / Esterase Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Cea-Rama, I. / Sanz-Aparicio, J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2021 Title: Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase. Authors: Cea-Rama, I. / Coscolin, C. / Katsonis, P. / Bargiela, R. / Golyshin, P.N. / Lichtarge, O. / Ferrer, M. / Sanz-Aparicio, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sya.cif.gz | 148.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sya.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/6sya ftp://data.pdbj.org/pub/pdb/validation_reports/sy/6sya | HTTPS FTP |
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-Related structure data
Related structure data | 6sxyC 6sxpS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 9 - 346 / Label seq-ID: 28 - 365
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-Components
#1: Protein | Mass: 40201.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A2K8JN75 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: 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: 2.19 Å3/Da / Density % sol: 43.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 28% PEG3000, 0.2M MgCl2x6H2O, 0.1M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2018 / Details: KB focusing mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→45.96 Å / Num. obs: 30378 / % possible obs: 99.4 % / Redundancy: 5.3 % / CC1/2: 0.953 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.081 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.27→2.34 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2810 / CC1/2: 0.839 / Rpim(I) all: 0.302 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SXP Resolution: 2.27→45.96 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.242 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.243 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.87 Å2 / Biso mean: 27.85 Å2 / Biso min: 14.6 Å2
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Refinement step | Cycle: final / Resolution: 2.27→45.96 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 11158 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.27→2.329 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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