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Yorodumi- PDB-4f96: Crystal Structure of VldE, the pseudo-glycosyltransferase, in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f96 | ||||||
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Title | Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP | ||||||
Components | VldE | ||||||
Keywords | TRANSFERASE / Twin Rossman Fold | ||||||
Function / homology | Function and homology information validamine 7-phosphate valienyltransferase / trehalose biosynthetic process / hexosyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces hygroscopicus subsp. limoneus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.152 Å | ||||||
Authors | Cavalier, M.C. / Yim, Y.-S. / Asamizu, S. / Neau, D. / Almabruk, K.H. / Mahmud, T. / Lee, Y.-H. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Mechanistic Insights into Validoxylamine A 7'-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex. Authors: Cavalier, M.C. / Yim, Y.S. / Asamizu, S. / Neau, D. / Almabruk, K.H. / Mahmud, T. / Lee, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f96.cif.gz | 204.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f96.ent.gz | 161.6 KB | Display | PDB format |
PDBx/mmJSON format | 4f96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f96_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4f96_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4f96_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 4f96_validation.cif.gz | 55.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/4f96 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/4f96 | HTTPS FTP |
-Related 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 domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 55006.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hygroscopicus subsp. limoneus (bacteria) Gene: vldE / Production host: Escherichia coli (E. coli) References: UniProt: Q15JG1, Transferases; Glycosyltransferases #2: Chemical | #3: Chemical | #4: 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: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris-HCl, pH 8.0, 30-35% PEG3350, 3 mM GDP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 2, 2012 |
Radiation | Monochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→37.77 Å / Num. all: 52004 / Num. obs: 51924 / % possible obs: 99.9 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 |
Reflection shell | Resolution: 2.15→2.23 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.152→37.524 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 20.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.866 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.152→37.524 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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