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Yorodumi- PDB-5m10: Crystal structure of cyclohexanone monooxygenase from Thermocrisp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m10 | ||||||
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Title | Crystal structure of cyclohexanone monooxygenase from Thermocrispum municipale in the oxidised state with a bound nicotinamide. | ||||||
Components | Cyclohexanone Monooxygenase from Thermocrispum municipale | ||||||
Keywords | OXIDOREDUCTASE / Cyclohexanone monooxygenase Baeyer-Villiger monooxygenases Flavoenzymes | ||||||
Function / homology | Function and homology information cyclohexanone monooxygenase / cyclohexanone monooxygenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Thermocrispum municipale (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Gomez-Castellanos, J.R. / Mattevi, A. | ||||||
Funding support | 1items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2016 Title: Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase. Authors: Romero, E. / Castellanos, J.R. / Mattevi, A. / Fraaije, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m10.cif.gz | 261.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m10.ent.gz | 206.8 KB | Display | PDB format |
PDBx/mmJSON format | 5m10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/5m10 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/5m10 | HTTPS FTP |
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-Related structure data
Related structure data | 5m0zC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m35m0z / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60195.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermocrispum municipale (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): str. K-12 substr. DH10B References: UniProt: A0A1L1QK40*PLUS, cyclohexanone monooxygenase |
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-Non-polymers , 6 types, 573 molecules
#2: Chemical | ChemComp-FAD / | ||||
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#3: Chemical | ChemComp-NAP / | ||||
#4: Chemical | ChemComp-NCA / | ||||
#5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl, 30 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 273.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→38.93 Å / Num. obs: 168622 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 9.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 8.36 |
Reflection shell | Resolution: 1.22→1.26 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 1.21 / CC1/2: 0.701 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→38.9 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.804 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.037 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.472 Å2
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Refinement step | Cycle: 1 / Resolution: 1.22→38.9 Å
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Refine LS restraints |
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