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Yorodumi- PDB-7v46: Crystal structure of Class I P450 monooxygenase (P450tol) from Rh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v46 | ||||||
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Title | Crystal structure of Class I P450 monooxygenase (P450tol) from Rhodococcus coprophilus TC-2 in complex with ortho-chlorotoluene. | ||||||
Components | p450tol monooxygenase | ||||||
Keywords | ELECTRON TRANSPORT / HEM | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Rhodococcus coprophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zhang, L.L. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Funding support | 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Molecular Basis for a Toluene Monooxygenase to Govern Substrate Selectivity Authors: Chen, C.C. / Dai, M. / Zhang, L. / Zhao, J. / Zeng, W. / Shi, M. / Huang, J.W. / Liu, W. / Guo, R.T. / Li, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v46.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v46.ent.gz | 85.9 KB | Display | PDB format |
PDBx/mmJSON format | 7v46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/7v46 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/7v46 | HTTPS FTP |
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-Related structure data
Related structure data | 7v40C 7v41C 7v42C 7v43C 7v44C 7v45C 1cptS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 49406.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus coprophilus (bacteria) / Plasmid: pRSF-Duet I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A088FL33 |
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#2: Chemical | ChemComp-C4U / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.08 % / Mosaicity: 0.219 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: Na/K phosphate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 10, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2 cooled Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→25 Å / Num. obs: 52983 / % possible obs: 98.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.367 / Rpim(I) all: 0.165 / Rrim(I) all: 0.405 / Χ2: 1.035 / Net I/σ(I): 12.6 / Num. measured all: 340514 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1cpt Resolution: 1.8→24.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.54 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.115 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 74.59 Å2 / Biso mean: 26.728 Å2 / Biso min: 15.64 Å2
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Refinement step | Cycle: final / Resolution: 1.8→24.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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