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Yorodumi- PDB-6b11: TylHI in complex with native substrate 23-deoxy-5-O-mycaminosyl-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b11 | ||||||
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Title | TylHI in complex with native substrate 23-deoxy-5-O-mycaminosyl-tylonolide (23-DMTL) | ||||||
Components | 20-oxo-5-O-mycaminosyltylactone 23-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / P450 / tylosin biosynthesis | ||||||
Function / homology | Function and homology information 20-oxo-5-O-mycaminosyltylactone 23-monooxygenase / antibiotic metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Streptomyces fradiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å | ||||||
Authors | DeMars, M.D. / Sherman, D.H. / Podust, L.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: TylHI in complex with native substrate 23-deoxy-5-O-mycaminosyl-tylonolide (23-DMTL) Authors: DeMars, M.D. / Sherman, D.H. / Podust, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b11.cif.gz | 177.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b11.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 6b11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/6b11 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/6b11 | HTTPS FTP |
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-Related structure data
Related structure data | 5foiS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47800.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CYS 41 is spontaneously oxidized to sulfenic acid (CSO) Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: tylH1, tylHI / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZHQ1, EC: 1.14.13.186 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 57.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14% PEG MME 550, 0.1 M HEPES, pH 7.5, 6 mM glutathione Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 9, 2016 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→88.47 Å / Num. obs: 69968 / % possible obs: 95.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.63 |
Reflection shell | Resolution: 1.99→2.04 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.74 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 7210 / % possible all: 69.7 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FOI Resolution: 1.99→88.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.829 / SU ML: 0.129 / SU R Cruickshank DPI: 0.1577 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.153 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.87 Å2 / Biso mean: 46.516 Å2 / Biso min: 19.54 Å2
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Refinement step | Cycle: final / Resolution: 1.99→88.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.985→2.037 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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