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Open data
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Basic information
Entry | Database: PDB / ID: 1iir | ||||||
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Title | Crystal Structure of UDP-glucosyltransferase GtfB | ||||||
![]() | glycosyltransferase GtfB | ||||||
![]() | TRANSFERASE / glycosyltransferase / rossmann fold | ||||||
Function / homology | ![]() vancomycin aglycone glucosyltransferase / vancomycin biosynthetic process / hexosyltransferase activity / lipid glycosylation / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mulichak, A.M. / Losey, H.C. / Walsh, C.T. / Garavito, R.M. | ||||||
![]() | ![]() Title: Structure of the UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics. Authors: Mulichak, A.M. / Losey, H.C. / Walsh, C.T. / Garavito, R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90 KB | Display | ![]() |
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PDB format | ![]() | 66.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.7 KB | Display | ![]() |
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Full document | ![]() | 435.6 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | Enzyme is a monomer. |
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Components
#1: Protein | Mass: 43777.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P96559, Transferases; Glycosyltransferases; Hexosyltransferases | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.39 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: magnesium sulfate, PEG 400, MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 8, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 41142 / Num. obs: 41091 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 5 / Num. unique all: 4040 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Missing residues 56-62, 140-148, 246-248, 402-415 are disordered and unobserved in crystal structure. Also, for some residues side chain atoms are disordered and omitted from refined ...Details: Missing residues 56-62, 140-148, 246-248, 402-415 are disordered and unobserved in crystal structure. Also, for some residues side chain atoms are disordered and omitted from refined coordinates (C8, R11, E41, R63, E92, I149, D150, Q160, R273, D282, D283).
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Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati sigma a obs: 0.13 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / σ(F): 1 / % reflection Rfree: 7.2 % / Rfactor obs: 0.211 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.294 / Rfactor Rwork: 0.241 |