+Open data
-Basic information
Entry | Database: PDB / ID: 3up4 | ||||||
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Title | Crystal Structure of OTEMO complex with FAD and NADP (form 3) | ||||||
Components | OTEMO(2,2,3-Trimethyl-5-oxocyclopent-3-enyl)acetyl-CoA 1,5-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Baeyer-Villiger monooxygenase | ||||||
Function / homology | Function and homology information (2,2,3-trimethyl-5-oxocyclopent-3-enyl)acetyl-CoA 1,5-monooxygenase / (+)-camphor catabolic process / FAD binding / monooxygenase activity / NADP binding / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å | ||||||
Authors | Shi, R. / Matte, A. / Cygler, M. / Lau, P. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2012 Title: Cloning, Baeyer-Villiger biooxidations, and structures of the camphor pathway 2-oxo-{Delta}(3)-4,5,5-trimethylcyclopentenylacetyl-coenzyme A monooxygenase of Pseudomonas putida ATCC 17453. Authors: Leisch, H. / Shi, R. / Grosse, S. / Morley, K. / Bergeron, H. / Cygler, M. / Iwaki, H. / Hasegawa, Y. / Lau, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3up4.cif.gz | 421.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3up4.ent.gz | 346.8 KB | Display | PDB format |
PDBx/mmJSON format | 3up4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/3up4 ftp://data.pdbj.org/pub/pdb/validation_reports/up/3up4 | HTTPS FTP |
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-Related structure data
Related structure data | 3uovC 3uoxC 3uoySC 3uozC 3up5C 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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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 61445.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: ATCC 17453 / Gene: otemo / Plasmid: pSD80 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H3JQW0*PLUS, Oxidoreductases #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: 2.33 Å3/Da / Density % sol: 47.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 22% PEG3350, 0.1 M sodium/potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 20, 2010 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.804→141.349 Å / Num. obs: 29210 / % possible obs: 88.2 % / Redundancy: 3.2 % / Rsym value: 0.128 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.804→2.9 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.52 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UOY Resolution: 2.804→48.315 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.862 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.634 / SU ML: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.98 Å2 / Biso mean: 29.1231 Å2 / Biso min: 5.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.804→48.315 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.804→2.877 Å / Total num. of bins used: 20
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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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