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Yorodumi- PDB-5ex9: Structure of P450 StaF from glycopeptide antibiotic A47934 biosyn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ex9 | ||||||
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Title | Structure of P450 StaF from glycopeptide antibiotic A47934 biosynthesis; glycerol cryo | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / monooxygenase / phenolic coupling / glycopeptide antibiotic biosynthesis | ||||||
Function / homology | Function and homology information 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 | Streptomyces toyocaensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cryle, M.J. / Ulrich, V. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Beilstein J Org Chem / Year: 2016 Title: Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934. Authors: Ulrich, V. / Brieke, C. / Cryle, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ex9.cif.gz | 191.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ex9.ent.gz | 151.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ex9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ex9_validation.pdf.gz | 821.5 KB | Display | wwPDB validaton report |
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Full document | 5ex9_full_validation.pdf.gz | 825.2 KB | Display | |
Data in XML | 5ex9_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 5ex9_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/5ex9 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/5ex9 | HTTPS FTP |
-Related structure data
Related structure data | 5ex8C 3o1aS 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
#1: Protein | Mass: 47337.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces toyocaensis (bacteria) / Gene: BU52_01275 / Plasmid: pET151 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KLL7 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 1.2 M NH4PO4, 0.3 M K2HPO4, 0.1 M NH4PO4 citrate (pH 4.2) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 33006 / % possible obs: 98.4 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Rsym value: 0.062 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.5 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O1A Resolution: 2.2→47.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.055 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.165 / 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: 36.062 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→47.51 Å
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Refine LS restraints |
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