+Open data
-Basic information
Entry | Database: PDB / ID: 4ypv | ||||||
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Title | High-resolution structure of a metagenome-derived esterase Est8 | ||||||
Components | Est8 | ||||||
Keywords | HYDROLASE / esterase / Est8 / metagenome / microbial consortium | ||||||
Function / homology | Alpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | Parvibaculum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Pereira, M.R. / Maester, C.T. / Macedo Lemos, E. / Hyvonen, M. / Balan, A. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: Appl. Microbiol. Biotechnol. / Year: 2017 Title: From a metagenomic source to a high-resolution structure of a novel alkaline esterase. Authors: Pereira, M.R. / Maester, T.C. / Mercaldi, G.F. / de Macedo Lemos, E.G. / Hyvonen, M. / Balan, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ypv.cif.gz | 137.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ypv.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ypv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ypv_validation.pdf.gz | 419.2 KB | Display | wwPDB validaton report |
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Full document | 4ypv_full_validation.pdf.gz | 422.1 KB | Display | |
Data in XML | 4ypv_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 4ypv_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/4ypv ftp://data.pdbj.org/pub/pdb/validation_reports/yp/4ypv | HTTPS FTP |
-Related structure data
Related structure data | 1evqS S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 37046.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parvibaculum (bacteria) / Gene: est8 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: carboxylesterase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 60.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1% PEG 8000, 1.4 M Triammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.919 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→27.985 Å / Num. obs: 35630 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.47 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.44 |
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.23 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EVQ Resolution: 1.85→27.985 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 17.12 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→27.985 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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