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Yorodumi- PDB-8agm: Limonene epoxide low pH soak of epoxide hydrolase from metagenomi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8agm | ||||||
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Title | Limonene epoxide low pH soak of 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 / D-LIMONENE 1,2-EPOXIDE / Alpha/beta epoxide hydrolase Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.966 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 | 8agm.cif.gz | 261.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8agm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8agm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8agm_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 8agm_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8agm_validation.xml.gz | 44.1 KB | Display | |
Data in CIF | 8agm_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/8agm ftp://data.pdbj.org/pub/pdb/validation_reports/ag/8agm | HTTPS FTP |
-Related structure data
Related structure data | 8agnC 8agpC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 34940.449 Da / Num. of mol.: 4 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 #2: Chemical | ChemComp-LEO / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / | #5: 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: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.5 Details: Morpheus crystal screen condition C3, 40% v/v Glycerol; 20% w/v PEG 4000 . The crystal was soaked for two hours in cryoprotectant containing 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) ...Details: Morpheus crystal screen condition C3, 40% v/v Glycerol; 20% w/v PEG 4000 . The crystal was soaked for two hours in cryoprotectant containing 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) isomers of (+)-limonene oxide at pH 4.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.966→96.129 Å / Num. obs: 91956 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.966→2 Å / Num. unique obs: 4525 / CC1/2: 0.322 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ng7 Resolution: 1.966→96.129 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.217 / ESU R Free: 0.185 / 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: 63.288 Å2
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Refinement step | Cycle: LAST / Resolution: 1.966→96.129 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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