[English] 日本語
![](img/lk-miru.gif)
- PDB-1orr: Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1orr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of CDP-Tyvelose 2-Epimerase complexed with NAD and CDP | ||||||
![]() | CDP-tyvelose-2-epimerase | ||||||
![]() | ISOMERASE / Rossmann fold / short-chain dehydrogenase/reductase | ||||||
Function / homology | ![]() CDP-paratose 2-epimerase / CDP-abequose epimerase activity / lipopolysaccharide biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koropatkin, N.M. / Liu, H. / Holden, H.M. | ||||||
![]() | ![]() Title: High Resolution X-ray Structure of Tyvelose Epimerase from Salmonella typhi Authors: Koropatkin, N.M. / Liu, H.W. / Holden, H.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 306.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 245.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 67 KB | Display | |
Data in CIF | ![]() | 95.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39138.090 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14169, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-CDP / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 39.95 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8000, succinate, tetramethylammonium chloride, CDP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Dec 4, 2002 / Details: mirrors |
Radiation | Monochromator: double crystal Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. all: 225494 / Num. obs: 225494 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.061 / Net I/σ(I): 40.8 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 21022 / Rsym value: 0.212 / % possible all: 89.2 |
Reflection | *PLUS Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 89.2 % / Redundancy: 2.8 % / Num. unique obs: 21022 / Rmerge(I) obs: 0.212 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 203000 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|