+Open data
-Basic information
Entry | Database: PDB / ID: 4rie | ||||||
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Title | Landomycin Glycosyltransferase LanGT2 | ||||||
Components | Glycosyl transferase homolog | ||||||
Keywords | TRANSFERASE / GT fold / glycosyltransferase | ||||||
Function / homology | Function and homology information cellular glucuronidation / UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / enzyme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces cyanogenus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 Å | ||||||
Authors | Tam, H.K. / Gerhardt, S. / Breit, B. / Bechthold, A. / Einsle, O. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Structural Characterization of O- and C-Glycosylating Variants of the Landomycin Glycosyltransferase LanGT2. Authors: Tam, H.K. / Harle, J. / Gerhardt, S. / Rohr, J. / Wang, G. / Thorson, J.S. / Bigot, A. / Lutterbeck, M. / Seiche, W. / Breit, B. / Bechthold, A. / Einsle, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rie.cif.gz | 272.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rie.ent.gz | 221.9 KB | Display | PDB format |
PDBx/mmJSON format | 4rie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rie_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 4rie_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 4rie_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 4rie_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/4rie ftp://data.pdbj.org/pub/pdb/validation_reports/ri/4rie | HTTPS FTP |
-Related structure data
Related structure data | 4rifC 4rigC 4rihC 4riiC 2p6pS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 40406.105 Da / Num. of mol.: 2 / Fragment: Glycosyltransferase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces cyanogenus (bacteria) / Strain: S136 / Gene: lanGT2 / Plasmid: pET21::langt2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9ZGC0 #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: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 1.3 M sodium citrate 0.1 M HEPES/NaOH, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→214.31 Å / Num. all: 37364 / Num. obs: 37364 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.043 / Net I/σ(I): 40.4 |
Reflection shell | Resolution: 2.16→2.28 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P6P Resolution: 2.162→65.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.692 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.208 / 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: 46.688 Å2
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Refinement step | Cycle: LAST / Resolution: 2.162→65.81 Å
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Refine LS restraints |
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