[English] 日本語
![](img/lk-miru.gif)
- PDB-1ep0: HIGH RESOLUTION CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ep0 | ||||||
---|---|---|---|---|---|---|---|
Title | HIGH RESOLUTION CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM | ||||||
![]() | DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE | ||||||
![]() | ISOMERASE / racemase / dTDP-4-dehydrorhamnose epimerase / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | ![]() dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Christendat, D. / Saridakis, V. / Bochkarev, A. / Pai, E.F. / Arrowsmith, C.H. / Edwards, A.M. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase from Methanobacterium thermoautotrophicum complexed with dTDP. Authors: Christendat, D. / Saridakis, V. / Dharamsi, A. / Bochkarev, A. / Pai, E.F. / Arrowsmith, C.H. / Edwards, A.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 51.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 37 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 363.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 365 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer constructed from Chain A and one symmetry related molecule. |
-
Components
#1: Protein | Mass: 21702.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PET15B / Production host: ![]() ![]() References: UniProt: O27818, dTDP-4-dehydrorhamnose 3,5-epimerase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.18 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 10 % Polyethylene glycol 4K, 0.1 M Sodium Acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K | |||||||||||||||
Crystal | *PLUS Density % sol: 46 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953733 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 180757 / Num. obs: 29180 / % possible obs: 99.7 % / Observed criterion σ(F): 5592 / Observed criterion σ(I): 150.7 / Redundancy: 8 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.105 / Num. unique all: 2877 / % possible all: 100 |
Reflection shell | *PLUS % possible obs: 99.5 % / Mean I/σ(I) obs: 9.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.5→25.66 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 501863.81 / Data cutoff high rms absF: 501863.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS 0.9 / Details: Simulated Annealing
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.1104 Å2 / ksol: 0.422673 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→25.66 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.7 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|