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Yorodumi- PDB-5aii: Discovery and characterization of thermophilic limonene-1,2-epoxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aii | ||||||
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Title | Discovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries. CH55-sample-PEG complex | ||||||
Components | LIMONENE-1,2-EPOXIDE HYDROLASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | UNIDENTIFIED (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Ferrandi, E. / Sayer, C. / Isupov, M.N. / Annovazzi, C. / Marchesi, C. / Iacobone, G. / Peng, X. / Bonch-Osmolovskaya, E. / Wohlgemuth, R. / Littlechild, J.A. / Montia, D. | ||||||
Citation | Journal: FEBS J. / Year: 2015 Title: Discovery and Characterization of Thermophilic Limonene-1,2-Epoxide Hydrolases from Hot Spring Metagenomic Libraries Authors: Ferrandi, E.E. / Sayer, C. / Isupov, M.N. / Annovazzi, C. / Marchesi, C. / Iacobone, G. / Peng, X. / Bonch-Osmolovskaya, E. / Wohlgemuth, R. / Littlechild, J.A. / Montia, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aii.cif.gz | 462.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aii.ent.gz | 387 KB | Display | PDB format |
PDBx/mmJSON format | 5aii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/5aii ftp://data.pdbj.org/pub/pdb/validation_reports/ai/5aii | HTTPS FTP |
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-Related structure data
Related structure data | 5aifC 5aigC 5aihC 1nwwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP
#1: Protein | Mass: 14639.479 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) UNIDENTIFIED (others) / Plasmid: PRHAM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): 10G / References: limonene-1,2-epoxide hydrolase |
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-Non-polymers , 9 types, 1910 molecules
#2: Chemical | ChemComp-PG4 / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PG5 / | #7: Chemical | ChemComp-PGE / #8: Chemical | ChemComp-HIS / | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Sequence details | GENBANK KP765710 |
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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: 2.35 Å3/Da / Density % sol: 47.19 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→104.2 Å / Num. obs: 336972 / % possible obs: 97.5 % / Observed criterion σ(I): 1.9 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.47→1.51 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NWW Resolution: 1.47→104.23 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.476 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 27.644 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→104.23 Å
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Refine LS restraints |
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