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Yorodumi- PDB-7tto: P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tto | ||||||||||||
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Title | P450 (OxyA) from kistamicin biosynthesis, mixed heme conformation | ||||||||||||
Components | cytochrome P450 hydroxylase | ||||||||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / peptide cyclase / NRPS-associated / glycopeptide antibiotic | ||||||||||||
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 | Actinomadura parvosata subsp. kistnae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Greule, A. / Izore, T. / Cryle, M.J. | ||||||||||||
Funding support | Australia, Germany, 3items
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Citation | Journal: Front Chem / Year: 2022 Title: The Cytochrome P450 OxyA from the Kistamicin Biosynthesis Cyclization Cascade is Highly Sensitive to Oxidative Damage. Authors: Greule, A. / Izore, T. / Machell, D. / Hansen, M.H. / Schoppet, M. / De Voss, J.J. / Charkoudian, L.K. / Schittenhelm, R.B. / Harmer, J.R. / 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 | 7tto.cif.gz | 186.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tto.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 7tto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tto_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7tto_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7tto_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 7tto_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/7tto ftp://data.pdbj.org/pub/pdb/validation_reports/tt/7tto | HTTPS FTP |
-Related structure data
Related structure data | 7ttaC 7ttbC 7ttpC 7ttqC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42778.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinomadura parvosata subsp. kistnae (bacteria) Gene: KIS93_04812 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress / References: UniProt: A0A2P9IBF7, Oxidoreductases |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.94 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT, pH 6.0, 25% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→44.705 Å / Num. obs: 50318 / % possible obs: 99.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 22.44 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.017 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 4 / Num. unique obs: 2374 / CC1/2: 0.938 / Rpim(I) all: 0.176 / Rrim(I) all: 0.57 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PHYRE Model Resolution: 1.6→44.7 Å / SU ML: 0.2046 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8023 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→44.7 Å
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Refine LS restraints |
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LS refinement shell |
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