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Open data
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Basic information
Entry | Database: PDB / ID: 5ysw | ||||||
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Title | Crystal Structure Analysis of Rif16 in complex with R-L | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / rifamycin / METAL BINDING PROTEIN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, F.W. / Qi, F.F. / Xiao, Y.L. / Zhao, G.P. / Li, S.Y. | ||||||
![]() | ![]() Title: Deciphering the late steps of rifamycin biosynthesis. Authors: Qi, F. / Lei, C. / Li, F. / Zhang, X. / Wang, J. / Zhang, W. / Fan, Z. / Li, W. / Tang, G.L. / Xiao, Y. / Zhao, G. / Li, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95 KB | Display | ![]() |
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PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ysmC ![]() 4oqsS 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: 48785.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: U-32 / Gene: AMED_0653 / Plasmid: pET28b / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-9LF / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.93 % / Mosaicity: 1.48 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: Magnesium chloride hexahydrate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: SIEMENS-NICOLET / Detector: CCD / Date: Nov 3, 2017 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→50 Å / Num. obs: 12806 / % possible obs: 98.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.049 / Rrim(I) all: 0.12 / Χ2: 0.968 / Net I/σ(I): 5.7 / Num. measured all: 74314 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OQS Resolution: 2.6→35.38 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.2532 / WRfactor Rwork: 0.1937 / FOM work R set: 0.8123 / SU B: 11.814 / SU ML: 0.261 / SU Rfree: 0.3772 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.377 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.87 Å2 / Biso mean: 37.57 Å2 / Biso min: 14 Å2
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Refinement step | Cycle: final / Resolution: 2.6→35.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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