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Open data
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Basic information
Entry | Database: PDB / ID: 5iki | ||||||
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Title | CYP106A2 WITH SUBSTRATE ABIETIC ACID | ||||||
![]() | Cytochrome P450(MEG) | ||||||
![]() | OXIDOREDUCTASE / MONO-OXYGENASE / CYTOCHROME P450 / 15-BETA-HYDROXYLASE | ||||||
Function / homology | ![]() steroid 15beta-monooxygenase / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Janocha, S. / Carius, Y. / Bernhardt, R. / Lancaster, C.R.D. | ||||||
![]() | ![]() Title: Crystal Structure of CYP106A2 in Substrate-Free and Substrate-Bound Form. Authors: Janocha, S. / Carius, Y. / Hutter, M. / Lancaster, C.R. / Bernhardt, R. #1: Journal: Chembiochem / Year: 2011 Title: Identification of CYP106A2 as a regioselective allylic bacterial diterpene hydroxylase. Authors: Bleif, S. / Hannemann, F. / Lisurek, M. / Von Kries, J.P. / Zapp, J. / Dietzen, M. / Antes, I. / Bernhardt, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.7 KB | Display | ![]() |
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PDB format | ![]() | 135.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 41.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yt3C ![]() 1f4tS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 4 - 409 / Label seq-ID: 4 - 409
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Components
#1: Protein | Mass: 47015.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q06069, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous, steroid 15beta-monooxygenase #2: Chemical | #3: Chemical | ChemComp-A9H / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: PEG 4000 AMMONIUM ACETATE SODIUM ACETATE TRIHYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→78.98 Å / Num. obs: 32407 / % possible obs: 94.93 % / Redundancy: 3.82 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.39 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.11 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.94 / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F4T Resolution: 2.4→78.73 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.552 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R: 0.67 / ESU R Free: 0.304 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.362 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→78.73 Å
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Refine LS restraints |
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