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Yorodumi- PDB-7ayx: Structure of the cytochrome P450 AryC from Streptomyces roseospor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ayx | ||||||
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Title | Structure of the cytochrome P450 AryC from Streptomyces roseosporus NRRL 15998 | ||||||
Components | Cytochrome P450 113A1 | ||||||
Keywords | CYTOSOLIC PROTEIN / CytC P450 / oxidase / arylomycin 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 filamentosus NRRL 15998 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | ||||||
Authors | Schneider, S. / Schaefers, F. / Gulder, T.A.M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Chemistry / Year: 2022 Title: Carrier Protein-Free Enzymatic Biaryl Coupling in Arylomycin A2 Assembly and Structure of the Cytochrome P450 AryC. Authors: Aldemir, H. / Shu, S. / Schaefers, F. / Hong, H. / Richarz, R. / Harteis, S. / Einsiedler, M. / Milzarek, T.M. / Schneider, S. / Gulder, T.A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ayx.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ayx.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ayx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ayx_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 7ayx_full_validation.pdf.gz | 470.5 KB | Display | |
Data in XML | 7ayx_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 7ayx_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/7ayx ftp://data.pdbj.org/pub/pdb/validation_reports/ay/7ayx | HTTPS FTP |
-Related structure data
Related structure data | 3zbyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45655.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces filamentosus NRRL 15998 (bacteria) Gene: SSGG_05588 / Production host: Escherichia coli (E. coli) / References: UniProt: D6AU61 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.77 Å3/Da / Density % sol: 67.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1M Hepes pH 7.0 2.4M ammoniumsulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→61.32 Å / Num. obs: 46292 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.981 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.184 / Χ2: 0.91 / Net I/av σ(I): 3.8 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.53→2.62 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.58 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4486 / CC1/2: 0.443 / Χ2: 0.88 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZBY Resolution: 2.53→61.32 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 16.222 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.56 Å2 / Biso mean: 50.595 Å2 / Biso min: 18.83 Å2
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Refinement step | Cycle: final / Resolution: 2.53→61.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.53→2.596 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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