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Yorodumi- PDB-5nfq: Novel epoxide hydrolases belonging to the alpha/beta hydrolases s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nfq | ||||||
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Title | Novel epoxide hydrolases belonging to the alpha/beta hydrolases superfamily in metagenomes from hot environments | ||||||
Components | epoxide hydrolase belonging to alpha/beta hydrolase superfamily metagenomic from Tomsk sample | ||||||
Keywords | HYDROLASE / Epoxide hydrolases / metagenomics / industrial biocatalysis / stereoselectivity / protein structure | ||||||
Function / homology | IMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Ferrandi, E.E. / De Rose, S.A. / Sayer, C. / Guazzelli, E. / Marchesi, C. / Saneei, V. / Isupov, M.N. / Littlechild, J.A. / Monti, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Front Bioeng Biotechnol / Year: 2018 Title: New Thermophilic alpha / beta Class Epoxide Hydrolases Found in Metagenomes From Hot Environments. Authors: Ferrandi, E.E. / Sayer, C. / De Rose, S.A. / Guazzelli, E. / Marchesi, C. / Saneei, V. / Isupov, M.N. / Littlechild, J.A. / Monti, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nfq.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nfq.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 5nfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nfq_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 5nfq_full_validation.pdf.gz | 472.9 KB | Display | |
Data in XML | 5nfq_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 5nfq_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/5nfq ftp://data.pdbj.org/pub/pdb/validation_reports/nf/5nfq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34019.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) / References: soluble epoxide hydrolase |
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-Non-polymers , 5 types, 325 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-IMD / | #6: Water | ChemComp-HOH / | |
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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: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: E8 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.03 M of each ethylene glycol 0.1 M MOPS/HEPES-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→39.36 Å / Num. obs: 35698 / % possible obs: 97.4 % / Redundancy: 6 % / Rsym value: 0.106 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.015 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2070 / CC1/2: 0.516 / % possible all: 78.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.36 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.083 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096
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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 mean: 22.127 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→39.36 Å
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Refine LS restraints |
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