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- PDB-1lg9: Crystal structure of OxyB, a Cytochrome P450 Implicated in an Oxi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lg9 | ||||||
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Title | Crystal structure of OxyB, a Cytochrome P450 Implicated in an Oxidative Phenol Coupling Reaction During Vancomycin Biosynthesis | ||||||
![]() | P450 monooxygenase | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 monooxygenase | ||||||
Function / homology | ![]() vancomycin biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pylypenko, O. / Zerbe, K. / Vitali, F. / Zhang, W. / Vrijbloed, J.W. / Robinson, J.A. / Schlichting, I. | ||||||
![]() | ![]() Title: Crystal Structure of OxyB, a Cytochrome P450 Implicated in an Oxidative Phenol Coupling Reaction during Vancomycin Biosynthesis. Authors: Zerbe, K. / Pylypenko, O. / Vitali, F. / Zhang, W. / Rouset, S. / Heck, M. / Vrijbloed, J.W. / Bischoff, D. / Bister, B. / Sussmuth, R.D. / Pelzer, S. / Wohlleben, W. / Robinson, J.A. / Schlichting, I. #1: ![]() Title: The Biosynthesis of Vancomycin-Type Glycopeptide Antibiotics - The Order of the Cyclization Steps Authors: Bischoff, D. / Pelzer, S. / Bister, B. / Nicholson, G.J. / Stockert, S. / Schirle, M. / Wohlleben, W. / Jung, G. / Suessmuth, R.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.4 KB | Display | ![]() |
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PDB format | ![]() | 71.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.5 KB | Display | ![]() |
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Full document | ![]() | 799.1 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lfkSC ![]() 1lgfC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44429.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.45 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, potassium chloride, K-Hepes, DTE, SP1066, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2→41 Å / Num. all: 30159 / Num. obs: 30159 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.086 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 5 / Num. unique all: 7413 / Rsym value: 0.313 / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 41 Å / Num. measured all: 177864 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.313 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LFK Resolution: 2→41 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1935742.86 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.9794 Å2 / ksol: 0.305818 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.6 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 28 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.264 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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