+Open data
-Basic information
Entry | Database: PDB / ID: 1iir | ||||||
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Title | Crystal Structure of UDP-glucosyltransferase GtfB | ||||||
Components | glycosyltransferase GtfB | ||||||
Keywords | TRANSFERASE / glycosyltransferase / rossmann fold | ||||||
Function / homology | Function and homology information vancomycin aglycone glucosyltransferase / vancomycin biosynthetic process / hexosyltransferase activity / lipid glycosylation / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Amycolatopsis orientalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å | ||||||
Authors | Mulichak, A.M. / Losey, H.C. / Walsh, C.T. / Garavito, R.M. | ||||||
Citation | Journal: Structure / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iir.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iir.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 1iir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iir_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 1iir_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 1iir_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1iir_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/1iir ftp://data.pdbj.org/pub/pdb/validation_reports/ii/1iir | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | Enzyme is a monomer. |
-Components
#1: Protein | Mass: 43777.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Strain: A82846 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.8→30 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber 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 |