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Yorodumi- PDB-7y9j: Crystal structure of P450 BM3-TMK from Bacillus megaterium in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y9j | ||||||
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Title | Crystal structure of P450 BM3-TMK from Bacillus megaterium in complex with 5-nitro-1,2-benzisoxazole | ||||||
Components | Bifunctional cytochrome P450/NADPH--P450 reductase | ||||||
Keywords | OXIDOREDUCTASE / synthesis / monooxygenase | ||||||
Function / homology | Function and homology information 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 | Priestia megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Wang, Q. / Zhang, L.L. / Liu, W.D. / Huang, J.-W. / Yang, Y. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | China, 1items
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Citation | Journal: Chinese J Catal / Year: 2023 Title: Engineering of a P450-based Kemp eliminase with a new mechanism Authors: Li, A. / Wang, Q. / Song, X. / Zhang, X. / Huang, J.W. / Chen, C.C. / Guo, R.T. / Wang, B. / Reetz, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y9j.cif.gz | 206.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y9j.ent.gz | 161.6 KB | Display | PDB format |
PDBx/mmJSON format | 7y9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/7y9j ftp://data.pdbj.org/pub/pdb/validation_reports/y9/7y9j | HTTPS FTP |
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-Related structure data
Related structure data | 7y9kC 4kpaS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53010.391 Da / Num. of mol.: 2 / Mutation: E5K,L76Y,F88G,T439K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Priestia megaterium (bacteria) Strain: ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19 Gene: cyp102A1, cyp102, BG04_163 / Plasmid: pRSF-DuetI / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase #2: Chemical | #3: Chemical | ChemComp-H5J / | #4: 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: 2.56 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25-30% PEG 3350, 0.1 M MgCl2, 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→25 Å / Num. obs: 92441 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.031 / Rrim(I) all: 0.071 / Χ2: 1.286 / Net I/σ(I): 12 / Num. measured all: 524891 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KPA Resolution: 1.83→24.73 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.06 Å2 / Biso mean: 39.4835 Å2 / Biso min: 19.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→24.73 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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