[English] 日本語
![](img/lk-miru.gif)
- PDB-1pn3: Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in comp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pn3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the acceptor substrate DVV. | |||||||||
![]() |
| |||||||||
![]() | TRANSFERASE/ANTIBIOTIC / GT-B GLYCOSYLTRANSFERASE / ROSSMANN FOLD / GLYCOPEPTIDE / VANCOMYCIN / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 156.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 126.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 836.6 KB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 47.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
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.) ![]() ![]() ![]() #2: Protein/peptide | ![]() Details: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4. Source: (natural) ![]() #3: Chemical | ChemComp-TYD / | #4: Sugar | ![]() 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 | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.23 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 5 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|