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Open data
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Basic information
Entry | Database: PDB / ID: 2ygx | ||||||
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Title | Structure of the mixed-function P450 MycG in P21 space group | ||||||
![]() | P-450-LIKE PROTEIN | ||||||
![]() | ELECTRON TRANSPORT / MYCINAMICIN BIOSYNTHESIS / METAL BINDING | ||||||
Function / homology | ![]() Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / antibiotic biosynthetic process / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, S. / Kells, P.M. / Rutaganira, F.U. / Sherman, D.H. / Podust, L.M. | ||||||
![]() | ![]() Title: Substrate Recognition by the Multifunctional Cytochrome P450 Mycg in Mycinamicin Hydroxylation and Epoxidation Reactions. Authors: Li, S. / Tietz, D.R. / Rutaganira, F.U. / Kells, P.M. / Anzai, Y. / Kato, F. / Pochapsky, T.C. / Sherman, D.H. / Podust, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324 KB | Display | ![]() |
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PDB format | ![]() | 262 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 60 KB | Display | |
Data in CIF | ![]() | 83.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y46C ![]() 2y5nC ![]() 2y5zC ![]() 2y98SC ![]() 2ycaC ![]() 3zsnC ![]() 4aw3C 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: 46556.762 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SIN / | #5: Water | ChemComp-HOH / | Nonpolymer details | PROTOPORPH | Sequence details | THE 6XHIS TAG AND THROMBIN CLEAVAGE SITE ARE ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.1 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.6M SUCCINIC ACID PH 7, 2% GLYCEROL, 0.0075MM CYMAL-7 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→161.98 Å / Num. obs: 68714 / % possible obs: 95.6 % / Observed criterion σ(I): 0.5 / Redundancy: 3.8 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.39→2.52 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 / % possible all: 76.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y98 Resolution: 2.39→80.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 8.045 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.595 / ESU R Free: 0.293 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.371 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→80.99 Å
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Refine LS restraints |
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