+Open data
-Basic information
Entry | Database: PDB / ID: 4lei | ||||||
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Title | Spinosyn Forosaminyltransferase SpnP | ||||||
Components | NDP-forosamyltransferase | ||||||
Keywords | TRANSFERASE / Glycosyltransferase | ||||||
Function / homology | Function and homology information UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Saccharopolyspora spinosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Isiorho, E.A. / Liu, H.-W. / Keatinge-Clay, A.K. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structural studies of the spinosyn forosaminyltransferase, SpnP. Authors: Isiorho, E.A. / Jeon, B.S. / Kim, N.H. / Liu, H.W. / Keatinge-Clay, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lei.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lei.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/4lei ftp://data.pdbj.org/pub/pdb/validation_reports/le/4lei | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 50502.125 Da / Num. of mol.: 2 / Fragment: UNP residues 17-455 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: spnP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ALN7 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 4.24 Details: 7 mM PSA, 46% (w/v) PEG 200, 0.6-3.0% (w/v) dextran sulfate MR 5,000, 0.2 M sodium chloride, 0.1 M phosphate citrate buffer, pH 4.24 , VAPOR DIFFUSION, SITTING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2013 |
Radiation | Monochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→114.81 Å / Num. all: 19214 / Num. obs: 18175 / % possible obs: 99.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.15→3.231 Å / % possible all: 95.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→114.81 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.809 / SU B: 24.83 / SU ML: 0.433 / Cross valid method: THROUGHOUT / ESU R Free: 0.577 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 60.668 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→114.81 Å
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