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Open data
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Basic information
Entry | Database: PDB / ID: 4yt3 | ||||||
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Title | CYP106A2 | ||||||
![]() | 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 REGIO-SELECTIVE 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 | ![]() | 184.4 KB | Display | ![]() |
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PDB format | ![]() | 144.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 52 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ikiC ![]() 1f4tS ![]() 4xzo S: Starting model for refinement C: citing same article ( |
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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: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 4 - 410 / Label seq-ID: 4 - 410
NCS oper: (Code: given Matrix: (0.9999, -0.01012, -0.004943), Vector: |
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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 | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 4.2 Details: PEG 4000, ammonium acetate, sodium acetate trihydrate PH range: 4.2 |
-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: 1.8→66.18 Å / Num. obs: 79257 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F4T Resolution: 1.8→66.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.548 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.394 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→66.18 Å
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Refine LS restraints |
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