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Yorodumi- PDB-4bf4: PikC D50N mutant in complex with the engineered cycloalkane subst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bf4 | ||||||
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Title | PikC D50N mutant in complex with the engineered cycloalkane substrate mimic bearing a termianl N,N-dimethylamino group | ||||||
Components | CYTOCHROME P450 HYDROXYLASE PIKC | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / PIKROMYCIN BIOSYNTHESIS | ||||||
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: 2.7 Å | ||||||
Authors | Podust, L.M. | ||||||
Citation | Journal: To be Published Title: Recognition of Synthetic Substrates by P450 Pikc Authors: 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 | 4bf4.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4bf4.ent.gz | 2 MB | Display | PDB format |
PDBx/mmJSON format | 4bf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bf4_validation.pdf.gz | 5.9 MB | Display | wwPDB validaton report |
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Full document | 4bf4_full_validation.pdf.gz | 6 MB | Display | |
Data in XML | 4bf4_validation.xml.gz | 228.3 KB | Display | |
Data in CIF | 4bf4_validation.cif.gz | 303.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/4bf4 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/4bf4 | HTTPS FTP |
-Related structure data
Related structure data | 3zpiC 4b7dC 4umzC 2bvjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 48267.758 Da / Num. of mol.: 16 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): HMS174(DE3) / References: UniProt: O87605 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | 1.7.6 5-CYCLODODEC | |
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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: 2.22 Å3/Da / Density % sol: 44.6 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 27% PEG3350, 0.2 M LI SULFATE, 0.1 M NA CACODILATE, PH 6.5 |
-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: Sep 29, 2012 / 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: 2.7→119.84 Å / Num. obs: 169609 / % possible obs: 97.4 % / Observed criterion σ(I): 1.5 / Redundancy: 2.1 % / Biso Wilson estimate: 63.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BVJ Resolution: 2.7→119.84 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.874 / SU B: 37.957 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / 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: 45.865 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→119.84 Å
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