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- PDB-7v43: Crystal structure of Class I P450 monooxygenase (P450tol) from Rh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7v43 | ||||||
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Title | Crystal structure of Class I P450 monooxygenase (P450tol) from Rhodococcus coprophilus TC-2 in complex with para-chlorotoluene. | ||||||
![]() | p450tol monooxygenase | ||||||
![]() | ELECTRON TRANSPORT / HEM | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, L.L. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.8 KB | Display | ![]() |
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PDB format | ![]() | 89.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7v40C ![]() 7v41C ![]() 7v42C ![]() 7v44C ![]() 7v45C ![]() 7v46C ![]() 1cptS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49406.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 728 molecules ![](data/chem/img/C4O.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-C4O / |
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#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-PO4 / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.61 % / Mosaicity: 0.292 ° |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.4→25 Å / Num. obs: 108878 / % possible obs: 96.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Χ2: 1.23 / Net I/σ(I): 11.5 / Num. measured all: 1190211 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CPT Resolution: 1.4→24.17 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.733 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.051 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: 68.09 Å2 / Biso mean: 16.149 Å2 / Biso min: 6.45 Å2
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Refinement step | Cycle: final / Resolution: 1.4→24.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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