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Yorodumi- PDB-2yca: Mixed-function P450 MycG in complex with mycinamicin III in P2121... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yca | ||||||
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Title | Mixed-function P450 MycG in complex with mycinamicin III 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 / 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 | MICROMONOSPORA GRISEORUBIDA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 2yca.cif.gz | 194.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yca.ent.gz | 152.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yca_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2yca_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2yca_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2yca_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/2yca ftp://data.pdbj.org/pub/pdb/validation_reports/yc/2yca | HTTPS FTP |
-Related structure data
Related structure data | 2y46C 2y5nC 2y5zC 2y98C 2ygxC 3zsnC 4aw3C 2y4h 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 , 5 types, 334 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-ZM3 / | ||||
#4: Chemical | #5: Chemical | ChemComp-SIN / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE BOND TO CYS 346 GLYCEROL (GOL): CRYO- ...PROTOPORPH |
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Sequence details | 6XHIS TAG AND THE THROMBIN CLEAVAGE SITE WERE ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.6 M SUCCINIC ACID, PH 7.0 . |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→81.17 Å / Num. obs: 43565 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y4H 2y4h Resolution: 1.8→162.33 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.238 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.114 / 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: 23.068 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→162.33 Å
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