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- PDB-1pnv: Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pnv | |||||||||
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Title | Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and Vancomycin | |||||||||
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![]() | TRANSFERASE/ANTIBIOTIC / GT-B GLYCOSYLTRANSFERASE / ROSSMANN FOLD / GLYCOPEPTIDE / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX | |||||||||
Function / homology | ![]() chloroorienticin B synthase / cellular glucuronidation / vancomycin biosynthetic process / UDP-glycosyltransferase activity / hexosyltransferase activity / lipid glycosylation / carbohydrate metabolic process / enzyme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mulichak, A.M. / Losey, H.C. / Lu, W. / Wawrzak, Z. / Walsh, C.T. / Garavito, R.M. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.2 KB | Display | ![]() |
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PDB format | ![]() | 122 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 44.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is a monomer. |
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Components
#1: Protein | Mass: 42773.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | ![]() Details: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8 AND 9) ON RESIDUE 4. Source: (natural) ![]() #3: Polysaccharide | vancosamine-(1-2)-beta-D-glucopyranose | #4: Chemical | ChemComp-TYD / | #5: Water | ChemComp-HOH / | Compound details | VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L- ...VANCOMYCIN | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.1 % |
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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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 36772 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.072 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Rsym value: 0.236 / % possible all: 98.3 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. obs: 30058 / % possible obs: 98.3 % / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS Rmerge(I) obs: 0.236 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 62.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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