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Yorodumi- PDB-2wi9: Selective oxidation of carbolide C-H bonds by engineered macrolid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wi9 | ||||||
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Title | Selective oxidation of carbolide C-H bonds by engineered macrolide P450 monooxygenase | ||||||
Components | CYTOCHROME P450 HYDROXYLASE PIKC | ||||||
Keywords | OXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / CYP107L1 / CYTOCHROME P450 / HEME / IRON / MACROLIDE MONOOXYGENASE / METAL-BINDING / MONOOXYGENASE / OXIDOREDUCTASE ANTIBIOTIC BIOSYNTHESIS / PIKC | ||||||
Function / homology | Function and homology information pikromycin synthase / macrolide biosynthetic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES VENEZUELAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Li, S. / Chaulagain, M.R. / Knauff, A.R. / Podust, L.M. / Montgomery, J. / Sherman, D.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Selective Oxidation of Carbolide C-H Bonds by an Engineered Macrolide P450 Mono-Oxygenase. Authors: Li, S. / Chaulagain, M.R. / Knauff, A.R. / Podust, L.M. / Montgomery, J. / Sherman, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wi9.cif.gz | 185.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wi9.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wi9_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 2wi9_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2wi9_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 2wi9_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/2wi9 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/2wi9 | HTTPS FTP |
-Related structure data
Related structure data | 2whwC 2c6hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 oper: (Code: given Matrix: (-0.99993, -0.01215, 0.00056), Vector: |
-Components
#1: Protein | Mass: 48181.641 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: O87605 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | 20 N-TERMINAL RESIDUES INCLUDING 6XHIS TAG ARE ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.1 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 15% PEG 4000, 0.1 M TRIS-HCL, PH 7.5; 200 MM MGCL2 |
-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 CCD / Detector: CCD / Date: Jul 2, 2007 / 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→50 Å / Num. obs: 68456 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 87.7 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.7 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C6H Resolution: 2→88.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.931 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.17 / 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: 31.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2→88.74 Å
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Refine LS restraints |
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