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Yorodumi- PDB-4yxf: MupS, a 3-oxoacyl (ACP) reductase involved in Mupirocin biosynthesis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yxf | ||||||
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Title | MupS, a 3-oxoacyl (ACP) reductase involved in Mupirocin biosynthesis | ||||||
Components | MupS | ||||||
Keywords | OXIDOREDUCTASE / 3-oxoacyl (ACP) reductase / mupirocin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Till, M. / Race, P.R. | ||||||
Citation | Journal: To Be Published Title: MupS, a 3-oxoacyl (ACP) reductase involved in Mupirocin biosynthesis Authors: Till, M. / Race, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yxf.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yxf.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 4yxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/4yxf ftp://data.pdbj.org/pub/pdb/validation_reports/yx/4yxf | HTTPS FTP |
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-Related structure data
Related structure data | 3osuS 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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Unit cell |
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-Components
#1: Protein | Mass: 27343.959 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: mupS / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RL53 #2: 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: 4.54 Å3/Da / Density % sol: 72.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Molecular dimensions morpheus screen well C6 - NPS ligands, EDO_P8K precipitant mix PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→81.475 Å / Num. all: 28109 / Num. obs: 28109 / % possible obs: 100 % / Redundancy: 8.8 % / Rpim(I) all: 0.065 / Rrim(I) all: 0.191 / Rsym value: 0.18 / Net I/av σ(I): 3.669 / Net I/σ(I): 10.6 / Num. measured all: 248741 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-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: 3OSU Resolution: 2.7→47.08 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2285 / WRfactor Rwork: 0.1825 / FOM work R set: 0.8535 / SU B: 7.735 / SU ML: 0.16 / SU R Cruickshank DPI: 0.331 / SU Rfree: 0.2603 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 123.54 Å2 / Biso mean: 42.012 Å2 / Biso min: 18.75 Å2
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Refinement step | Cycle: final / Resolution: 2.7→47.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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