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- PDB-2y5z: Mixed-function P450 MycG in complex with mycinamicin III in C2221... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y5z | ||||||
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Title | Mixed-function P450 MycG in complex with mycinamicin III in C2221 space group | ||||||
![]() | P-450-LIKE PROTEIN | ||||||
![]() | OXIDOREDUCTASE / MYCINAMICIN BIOSYNTHESIS | ||||||
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. / 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 | ![]() | 520.3 KB | Display | ![]() |
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PDB format | ![]() | 427.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 56.1 KB | Display | |
Data in CIF | ![]() | 79.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y46C ![]() 2y5nC ![]() 2y98C ![]() 2ycaC ![]() 2ygxC ![]() 3zsnC ![]() 4aw3C ![]() 2y4h 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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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ZM3 / End label comp-ID: ZM3 / Refine code: 4 / Auth seq-ID: 5 - 460 / Label seq-ID: 25
NCS oper:
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 46556.762 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 810 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/ZM3.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZM3.gif)
![](data/chem/img/BEN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME-THIOLATE BOND TO CYS 346. MYCINAMICIN III (ZM3): ...PROTOPORPH |
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Sequence details | 6XHIS TAG AND THE THROMBIN CLEAVAGE SITE WERE ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.3 % / Description: NONE |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 7 Details: 12.5% PEG MME 5000, 6% TACSIMATE, PH 7.0, 2% BENZAMIDINE HYDROCHLORIDE, 0.15 M NACL; TEMPERATURE 23 DEGREES CELSIUS. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 20, 2010 / 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: 2.06→146.46 Å / Num. obs: 69912 / % possible obs: 86.3 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.06→2.17 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.5 / % possible all: 42.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y4H ![]() 2y4h Resolution: 2.06→219.68 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.228 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. JAVOSE SUGAR MOIETY OF THE MYCINAMICIN III SUBSTRATE IS DISORDERED.
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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: 28.339 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→219.68 Å
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Refine LS restraints |
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