[English] 日本語
![](img/lk-miru.gif)
- PDB-1ker: The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) fr... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ker | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose bound | ||||||
![]() | dTDP-D-glucose 4,6-dehydratase | ||||||
![]() | LYASE / Rossmann fold | ||||||
Function / homology | ![]() dTDP-glucose 4,6-dehydratase / UDP-L-rhamnose synthase activity / UDP-glucose 4,6-dehydratase activity / UDP-rhamnose biosynthetic process / dTDP-glucose 4,6-dehydratase activity / flavonol biosynthetic process / dTDP-rhamnose biosynthetic process / lipopolysaccharide biosynthetic process / extracellular polysaccharide biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Allard, S.T.M. / Beis, K. / Giraud, M.-F. / Hegeman, A.D. / Gross, J.W. / Whitfield, C. / Graninger, M. / Messner, P. / Allen, A.G. / Naismith, J.H. | ||||||
![]() | ![]() Title: Toward a structural understanding of the dehydratase mechanism. Authors: Allard, S.T. / Beis, K. / Giraud, M.F. / Hegeman, A.D. / Gross, J.W. / Wilmouth, R.C. / Whitfield, C. / Graninger, M. / Messner, P. / Allen, A.G. / Maskell, D.J. / Naismith, J.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 170.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 132.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 686.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 697.3 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kepC ![]() 1ketC ![]() 1keuC ![]() 1kewC ![]() 1g1aS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38982.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P95780, UniProt: Q8GIP9*PLUS, dTDP-glucose 4,6-dehydratase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.36 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 30% w/v PEG 8000, 0.1M sodium cacodylate pH 5.4, 0.2M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2001 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.7 Å / Num. obs: 55517 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.232 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.112 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / Num. unique all: 8000 / Rsym value: 0.284 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 179806 / Rmerge(I) obs: 0.112 |
Reflection shell | *PLUS % possible obs: 99.9 % / Num. unique obs: 8000 / Num. measured obs: 26125 / Rmerge(I) obs: 0.284 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB 1G1A Resolution: 2.2→49.7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Displacement parameters | Biso mean: 17.17 Å2 | ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→49.7 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.28 Å
| ||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 49.7 Å / % reflection Rfree: 10 % / Rfactor obs: 0.175 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.218 / Rfactor Rwork: 0.189 |