+Open data
-Basic information
Entry | Database: PDB / ID: 7q9e | ||||||
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Title | CYP106A1 | ||||||
Components | Cytochrome P450 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Cytochrome P450 / Steroid dehydrogenation | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / 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 | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Carius, Y. / Hutter, M. / Kiss, F. / Bernhardt, R. / Lancaster, C.R.D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Febs Lett. / Year: 2022 Title: Structural comparison of the cytochrome P450 enzymes CYP106A1 and CYP106A2 provides insight into their differences in steroid conversion. Authors: Carius, Y. / Hutter, M. / Kiss, F. / Bernhardt, R. / Lancaster, C.R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q9e.cif.gz | 349.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q9e.ent.gz | 282.2 KB | Display | PDB format |
PDBx/mmJSON format | 7q9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/7q9e ftp://data.pdbj.org/pub/pdb/validation_reports/q9/7q9e | HTTPS FTP |
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-Related structure data
Related structure data | 7zzlC 4yt3S 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 48459.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (strain DSM 319) (bacteria) Strain: DSM 319 / Gene: BMD_1855 / Production host: Escherichia coli (E. coli) References: UniProt: D5DF35, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: D5DF35, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor |
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-Non-polymers , 8 types, 1051 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-DMS / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-IMD / | #8: Chemical | ChemComp-PEO / | #9: Water | ChemComp-HOH / | |
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-Details
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: 2.3 Å3/Da / Density % sol: 46.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, lithium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97916 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25.92 Å / Num. obs: 168988 / % possible obs: 88.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Net I/σ(I): 7.05 |
Reflection shell | Resolution: 1.7→1.79 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 23968 / CC1/2: 0.92 / Rpim(I) all: 0.199 / Rrim(I) all: 0.367 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YT3 Resolution: 1.7→25.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.118 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / 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: 89.25 Å2 / Biso mean: 22.634 Å2 / Biso min: 7.36 Å2
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Refinement step | Cycle: final / Resolution: 1.7→25.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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