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Yorodumi- PDB-2y98: Structure of the mixed-function P450 MycG in complex with mycinam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y98 | ||||||
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Title | Structure of the mixed-function P450 MycG in complex with mycinamicin IV in P21212 space group | ||||||
Components | P-450-LIKE PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / MYCINAMICIN BIOSYNTHESIS | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / 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 | MICROMONOSPORA GRISEORUBIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Li, S. / Kells, P.M. / Sherman, D.H. / Podust, L.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y98.cif.gz | 197.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y98.ent.gz | 154.7 KB | Display | PDB format |
PDBx/mmJSON format | 2y98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/2y98 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/2y98 | HTTPS FTP |
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-Related structure data
Related structure data | 2y46C 2y5nC 2y5zC 2ycaC 2ygxC 3zsnC 4aw3C 2z36S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46556.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MICROMONOSPORA GRISEORUBIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59523 |
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-Non-polymers , 6 types, 404 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-MIV / | ||||
#4: Chemical | ChemComp-CL / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE BOND TO CYS 346 MYCINAMICIN IV (MIV): NATIVE ...PROTOPORPH |
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Sequence details | THE 6XHIS TAG AND THROMBIN CLEAVAGE SITE ARE ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % / Description: NONE |
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Crystal grow | Temperature: 296 K / pH: 5.5 Details: 8% PEG 4000, 0.2 M AMMONIUM SULFATE, 0.1 M BISTRIS PH 5.5, TEMP 23 C |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2009 / 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: 1.65→81.01 Å / Num. obs: 47944 / % possible obs: 84.9 % / Observed criterion σ(I): 1.5 / Redundancy: 6.4 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.6 / % possible all: 40.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z36 Resolution: 1.65→162.02 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.521 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.105 / 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: 20.986 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→162.02 Å
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Refine LS restraints |
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