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- PDB-3h4t: Chimeric Glycosyltransferase for the generation of novel natural ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h4t | ||||||
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Title | Chimeric Glycosyltransferase for the generation of novel natural products - GtfAH1 in complex with UDP-2F-Glc | ||||||
![]() | Glycosyltransferase GtfA, Glycosyltransferase | ||||||
![]() | TRANSFERASE / glycosyltransferase / vancomycin / teicoplanin / GtfA / orf1 / natural products / antibiotic | ||||||
Function / homology | ![]() chloroorienticin B synthase / cellular glucuronidation / vancomycin biosynthetic process / UDP-glycosyltransferase activity / hexosyltransferase activity / lipid glycosylation / acyltransferase activity / ligase activity / carbohydrate metabolic process / nucleotide binding / enzyme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dias, M.V.B. / Truman, A.W. / Wu, S. / Blundell, T.L. / Huang, F. / Spencer, J.B. | ||||||
![]() | ![]() Title: Chimeric glycosyltransferases for the generation of hybrid glycopeptides Authors: Truman, A.W. / Dias, M.V.B. / Wu, S. / Blundell, T.L. / Huang, F. / Spencer, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175 KB | Display | ![]() |
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PDB format | ![]() | 137.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3h4iC ![]() 1pn3S C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 42107.586 Da / Num. of mol.: 1 / Fragment: UNP residues 1-214, UNP residues 218-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GtfA / Plasmid: pET 28a(+) / Production host: ![]() ![]() References: UniProt: P96558, UniProt: Q6ZZJ7, Transferases; Glycosyltransferases | ||||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-UDP / | #4: Water | ChemComp-HOH / | Sequence details | THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE ONE(P96558 IN UNIPROT). ...THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND DATABASE REFERENCE ONE(P96558 IN UNIPROT). ACCORDING TO THE DEPOSITORS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.14 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris HCl pH 8.5, 1.2-2M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Dec 6, 2007 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→42.8 Å / Num. obs: 169485 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.077 / Num. measured all: 1154832 |
Reflection shell | Resolution: 1.15→1.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.647 / Num. measured all: 23415 / Num. unique all: 130919 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PN3 Resolution: 1.15→42.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.905 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.033 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 13.102 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→42.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.18 Å / Total num. of bins used: 20
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