+Open data
-Basic information
Entry | Database: PDB / ID: 7dls | ||||||
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Title | Cytochrome P450 (CYP105D18) complex with papaverine | ||||||
Components | Cytochrome P450 hydroxylase | ||||||
Keywords | TRANSFERASE / papaverine N-oxide / eukaryotic cytochrome P450 / chemical modification / heme oxidation | ||||||
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 | Streptomyces laurentii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Do, H. / Lee, J.H. | ||||||
Citation | Journal: Iucrj / Year: 2021 Title: Characterization of high-H 2 O 2 -tolerant bacterial cytochrome P450 CYP105D18: insights into papaverine N-oxidation. Authors: Pardhe, B.D. / Do, H. / Jeong, C.S. / Kim, K.H. / Lee, J.H. / Oh, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dls.cif.gz | 96.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dls.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dls_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7dls_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7dls_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 7dls_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/7dls ftp://data.pdbj.org/pub/pdb/validation_reports/dl/7dls | HTTPS FTP |
-Related structure data
Related structure data | 7di3SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44403.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces laurentii (bacteria) / Gene: SLA_5925 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A160P685 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-EV1 / |
#4: 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: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 1.5 M Ammonium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 41490 / % possible obs: 94.15 % / Redundancy: 4.7 % / CC1/2: 1 / Net I/σ(I): 17.05 |
Reflection shell | Resolution: 2.06→2.1 Å / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DI3 Resolution: 2.06→44.59 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.128 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.61 Å2 / Biso mean: 32.834 Å2 / Biso min: 14.81 Å2
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Refinement step | Cycle: final / Resolution: 2.06→44.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.064→2.117 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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