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- PDB-5jtd: Crystal structure of the Ru(bpy)2PhenA functionalized P450 BM3 L4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jtd | ||||||
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Title | Crystal structure of the Ru(bpy)2PhenA functionalized P450 BM3 L407C heme domain mutant in complex with DMSO. | ||||||
![]() | Bifunctional cytochrome P450/NADPH--P450 reductase | ||||||
![]() | OXIDOREDUCTASE / hybrid P450 BM3 enzymes / electron transfer / photosensitizer / photocatalytic activity | ||||||
Function / homology | ![]() NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kloos, M. | ||||||
![]() | ![]() Title: Insights into an efficient light-driven hybrid P450 BM3 enzyme from crystallographic, spectroscopic and biochemical studies. Authors: Spradlin, J. / Lee, D. / Mahadevan, S. / Mahomed, M. / Tang, L. / Lam, Q. / Colbert, A. / Shafaat, O.S. / Goodin, D. / Kloos, M. / Kato, M. / Cheruzel, L.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218 KB | Display | ![]() |
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PDB format | ![]() | 170.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 41 KB | Display | |
Data in CIF | ![]() | 60.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jq2C ![]() 1jpzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53685.062 Da / Num. of mol.: 2 / Mutation: L407C Source method: isolated from a genetically manipulated source Details: A Ru(bpy)2)PhenA was covalently attached to a non-native single cysteine (L407C) mutant of P450 BM3 mutant (post translational modification) Source: (gene. exp.) ![]() Strain: ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512 Gene: cyp102A1, cyp102, BG04_163 / Plasmid: pC-Wori / Production host: ![]() ![]() References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase #2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 150 mM MgCl2, 125 mM Na-MOPS, 20% PEG 3350, cryo: 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→47.36 Å / Num. obs: 183724 / % possible obs: 79.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 24.898 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.61 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Phasing MR | Packing: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JPZ Resolution: 1.5→47.36 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.554 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0705 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY ALTERNATIVE CONFORMATION OF HEM 460 AND RES 267-269 WERE DETECTED IN BOTH CHAINS BUT NOT MODELLED. WE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY ALTERNATIVE CONFORMATION OF HEM 460 AND RES 267-269 WERE DETECTED IN BOTH CHAINS BUT NOT MODELLED. WE OBSERVED DIFFERENCE DENSITY CLOSE TO THE RU8-LIGANDS WHICH MIGHT EITHER RESULT FROM THEIR STATIC DISORDER, OR ALTERNATIV CONFORMATION DUE TO A PHOTOSENSITIZER-ISOMER WHICH WAS COVALENTLY ATTACHED.
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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 max: 74.9 Å2 / Biso mean: 22.68 Å2 / Biso min: 11.22 Å2
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Refinement step | Cycle: final / Resolution: 1.5→47.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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