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Yorodumi- PDB-6era: Crystal structure of cyclohexanone monooxygenase mutant (F249A, F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6era | ||||||
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Title | Crystal structure of cyclohexanone monooxygenase mutant (F249A, F280A and F435A) from Rhodococcus sp. Phi1 bound to NADP+ | ||||||
Components | Cyclohexanone monooxygenase | ||||||
Keywords | FLAVOPROTEIN / Monooxygenase / Rossmann fold / FAD / NADP+ / lactone / dihydrocarvone | ||||||
Function / homology | Function and homology information N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Rhodococcus sp. Phi1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Karuppiah, V. / Scrutton, N.S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Biocatalytic Routes to Lactone Monomers for Polymer Production. Authors: Messiha, H.L. / Ahmed, S.T. / Karuppiah, V. / Suardiaz, R. / Ascue Avalos, G.A. / Fey, N. / Yeates, S. / Toogood, H.S. / Mulholland, A.J. / Scrutton, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6era.cif.gz | 429.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6era.ent.gz | 354.8 KB | Display | PDB format |
PDBx/mmJSON format | 6era.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6era_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6era_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6era_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 6era_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/6era ftp://data.pdbj.org/pub/pdb/validation_reports/er/6era | HTTPS FTP |
-Related structure data
Related structure data | 6er9C 3gwdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60711.430 Da / Num. of mol.: 2 / Mutation: F249A, F280A, F435A Source method: isolated from a genetically manipulated source Details: Mutations - F249A, F280A and F435A / Source: (gene. exp.) Rhodococcus sp. Phi1 (bacteria) / Gene: chnB / Production host: Escherichia coli (E. coli) / References: UniProt: Q84H73 #2: Chemical | #3: Chemical | #4: 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: 2.68 Å3/Da / Density % sol: 54.13 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→62.06 Å / Num. obs: 45368 / % possible obs: 99.8 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.045 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.49→2.53 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2228 / CC1/2: 0.587 / Rpim(I) all: 0.525 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GWD Resolution: 2.49→62.06 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.74 / Phase error: 29.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→62.06 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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