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Yorodumi- PDB-3ejb: Crystal Structure of P450BioI in complex with tetradecanoic acid ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ejb | ||||||
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Title | Crystal Structure of P450BioI in complex with tetradecanoic acid ligated Acyl Carrier Protein | ||||||
Components |
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Keywords | Oxidoreductase/Lipid Transport / Protein-Protein Complex / Cytochrome P450 Fold / Carrier Protein / 4-Helix Bundle / Fatty acid biosynthesis / Lipid synthesis / Phosphopantetheine / Biotin biosynthesis / Heme / Iron / Metal-binding / Monooxygenase / Oxidoreductase / Oxidoreductase-Lipid Transport COMPLEX | ||||||
Function / homology | Function and homology information pimeloyl-[acyl-carrier protein] synthase / biotin biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / acyl binding / acyl carrier activity / monooxygenase activity / fatty acid biosynthetic process ...pimeloyl-[acyl-carrier protein] synthase / biotin biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / acyl binding / acyl carrier activity / monooxygenase activity / fatty acid biosynthetic process / response to xenobiotic stimulus / iron ion binding / lipid binding / heme binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Cryle, M.J. / Schlichting, I. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex. Authors: Cryle, M.J. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ejb.cif.gz | 405.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ejb.ent.gz | 329.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ejb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ejb_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 3ejb_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 3ejb_validation.xml.gz | 84.9 KB | Display | |
Data in CIF | 3ejb_validation.cif.gz | 117.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/3ejb ftp://data.pdbj.org/pub/pdb/validation_reports/ej/3ejb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | heterodimers are formed by chain A and B, C and D, E and F, G and H. |
-Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 10685.630 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: acpP, b1094, JW1080 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P0A6A8 #2: Protein | Mass: 45988.352 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: GP208 / Gene: bioI, CYP107H, BSU30190 / Plasmid: pET24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P53554, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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-Sugars , 1 types, 8 molecules
#4: Sugar | ChemComp-HTG / |
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-Non-polymers , 4 types, 1348 molecules
#3: Chemical | ChemComp-ZMP / #5: Chemical | ChemComp-HEM / #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Na HEPES, 0.25 M NaCl, 0.15 M Li2SO4, 19% PEG 4000, 0.2% n-heptyl b-D-thioglucopyranoside, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98089 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2008 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98089 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 149113 / Num. obs: 144447 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.0604 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 7.4 / Rsym value: 0.33 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: SAD Structure Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.965 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.187 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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