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Yorodumi- PDB-1pn3: Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pn3 | |||||||||
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Title | Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the acceptor substrate DVV. | |||||||||
Components |
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Keywords | TRANSFERASE/ANTIBIOTIC / GT-B GLYCOSYLTRANSFERASE / ROSSMANN FOLD / GLYCOPEPTIDE / VANCOMYCIN / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX | |||||||||
Function / homology | Function and homology information chloroorienticin B synthase / vancomycin biosynthetic process / UDP-glycosyltransferase activity / hexosyltransferase activity / lipid glycosylation / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | AMYCOLATOPSIS ORIENTALIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | |||||||||
Authors | Mulichak, A.M. / Losey, H.C. / Lu, W. / Wawrzak, Z. / Walsh, C.T. / Garavito, R.M. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Structure of the Tdp-Epi-Vancosaminyltransferase Gtfa from the Chloroeremomycin Biosynthetic Pathway. Authors: Mulichak, A.M. / Losey, H.C. / Lu, W. / Wawrzak, Z. / 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 | 1pn3.cif.gz | 156.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pn3.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/1pn3 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/1pn3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a monomer. |
-Components
#1: Protein | Mass: 42773.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Gene: GTFA / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P96558 #2: Protein/peptide | Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4. Source: (natural) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00681, DESVANCOSAMINYL VANCOMYCIN #3: Chemical | ChemComp-TYD / | #4: Sugar | Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic / Mass: 180.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C6H12O6 Details: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4. References: DESVANCOSAMINYL VANCOMYCIN #5: Water | ChemComp-HOH / | Compound details | VANCOMYCIN DESVANCOSAMINYL IS A TRICYCLIC GLYCOPEPTIDE, A MEMBER OF THE VANCOMYCIN FAMILY. THE ...VANCOMYCIN | |
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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: 3.87 Å3/Da / Density % sol: 68.23 % |
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Crystal grow | pH: 6.1 Details: NA,K PHOSPHATE, PH 6.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
Crystal grow | *PLUS Method: vapor diffusion, hanging drop |
Components of the solutions | *PLUS Conc.: 1.3 M / Common name: sodium potassium phosphate / Details: pH6.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 31308 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.081 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6 % / Rsym value: 0.295 / % possible all: 99.8 |
Reflection | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS Rmerge(I) obs: 0.295 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 44.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor all: 5 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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