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Open data
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Basic information
Entry | Database: PDB / ID: 3abb | ||||||
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Title | Crystal structure of CYP105D6 | ||||||
![]() | Cytochrome P450 hydroxylase | ||||||
![]() | OXIDOREDUCTASE / P450 / heme / monooxygenase / macrolide / filipin / Iron / Metal-binding | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, L.H. / Fushinobu, S. / Takamatsu, S. / Wakagi, T. / Ikeda, H. / Shoun, H. | ||||||
![]() | ![]() Title: Regio- and stereospecificity of filipin hydroxylation sites revealed by crystal structures of cytochrome P450 105P1 and 105D6 from Streptomyces avermitilis Authors: Xu, L.H. / Fushinobu, S. / Takamatsu, S. / Wakagi, T. / Ikeda, H. / Shoun, H. #1: ![]() Title: Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis: conformational flexibility and histidine ligation state Authors: Xu, L.H. / Fushinobu, S. / Ikeda, H. / Wakagi, T. / Shoun, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.9 KB | Display | ![]() |
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PDB format | ![]() | 71.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 801.2 KB | Display | ![]() |
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Full document | ![]() | 811.3 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3abaC ![]() 1uedS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44576.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q79ZT5, UniProt: Q93H80*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of ...References: UniProt: Q79ZT5, UniProt: Q93H80*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Sodium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 13, 2007 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 22279 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UED Resolution: 2.3→33.77 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.023 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.716 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2557 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→33.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.358 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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