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Yorodumi- PDB-8agp: Halogenated product of limonene epoxide turnover by epoxide hydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8agp | ||||||
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Title | Halogenated product of limonene epoxide turnover by epoxide hydrolase from metagenomic source ch65 | ||||||
Components | Alpha/beta epoxide hydrolase | ||||||
Keywords | HYDROLASE / Alpha/beta hydrolase fold / complex with substrate / limonene epoxide | ||||||
Function / homology | Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Chem-M1U / Alpha/beta epoxide hydrolase Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Isupov, M.N. / De Rose, S.A. / Mitchell, D. / Littlechild, J.A. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Complexes of epoxide hydrolase from metagenomic source ch65 Authors: Isupov, M.N. / De Rose, S.A. / Mitchell, D. / Littlechild, J.A. / Parker, E. / Ferrandi, E. / Guazzelli, E. / Monti, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8agp.cif.gz | 157.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8agp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8agp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8agp_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8agp_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8agp_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 8agp_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8agp ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8agp | HTTPS FTP |
-Related structure data
Related structure data | 8agmC 8agnC 8agsC 5ng7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 289 / Label seq-ID: 4 - 289
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 34940.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A1U9WZ52 |
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-Non-polymers , 5 types, 449 molecules
#2: Chemical | ChemComp-M1U / ( #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.09 Å3/Da / Density % sol: 41.12 % |
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Crystal grow | Temperature: 291 K / Method: microbatch Details: Morpheus crystallisation kit condition C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000. The crystal was incubated with 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) isomers of (+)-limonene ...Details: Morpheus crystallisation kit condition C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000. The crystal was incubated with 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) isomers of (+)-limonene oxide for 1 hour 20 mins to produce a halogenated product in the active site. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→51.263 Å / Num. obs: 93810 / % possible obs: 99.1 % / Redundancy: 3.2 % / CC1/2: 0.998 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.49→1.52 Å / Num. unique obs: 4644 / CC1/2: 0.366 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ng7 Resolution: 1.49→51.263 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.108 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.083 / Details: Hydrogens have not been used
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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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.938 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→51.263 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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