[English] 日本語
Yorodumi- PDB-3h4t: Chimeric Glycosyltransferase for the generation of novel natural ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h4t | ||||||
---|---|---|---|---|---|---|---|
Title | Chimeric Glycosyltransferase for the generation of novel natural products - GtfAH1 in complex with UDP-2F-Glc | ||||||
Components | Glycosyltransferase GtfA, Glycosyltransferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase / vancomycin / teicoplanin / GtfA / orf1 / natural products / antibiotic | ||||||
Function / homology | Function and homology information 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 | Amycolatopsis orientalis (bacteria) Actinoplanes teichomyceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Dias, M.V.B. / Truman, A.W. / Wu, S. / Blundell, T.L. / Huang, F. / Spencer, J.B. | ||||||
Citation | Journal: Chem.Biol. / Year: 2009 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3h4t.cif.gz | 175 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3h4t.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 3h4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h4t_validation.pdf.gz | 785.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3h4t_full_validation.pdf.gz | 789.5 KB | Display | |
Data in XML | 3h4t_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 3h4t_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/3h4t ftp://data.pdbj.org/pub/pdb/validation_reports/h4/3h4t | HTTPS FTP |
-Related structure data
Related structure data | 3h4iC 1pn3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-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.) Amycolatopsis orientalis (bacteria), (gene. exp.) Actinoplanes teichomyceticus (bacteria) Gene: GtfA / Plasmid: pET 28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P96558, UniProt: Q6ZZJ7, Transferases; Glycosyltransferases | ||||||
---|---|---|---|---|---|---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.14 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.977 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→42.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.15→1.18 Å / Total num. of bins used: 20
|