[English] 日本語
![](img/lk-miru.gif)
- PDB-3lm7: Crystal Structure of DUF1341 representative, from Yersinia entero... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3lm7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of DUF1341 representative, from Yersinia enterocolitica subsp. enterocolitica 8081 | ||||||
![]() | putative 4-Hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxyphosphogluconate aldolase | ||||||
![]() | LYASE / putative 4-Hydroxy-oxoglutarate aldolase / 2-dehydro-3-deoxyphosphogluconate aldolase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joachimiak, A. / Duke, N.E.C. / Feldmann, B. / Wu, R. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal Structure of DUF1341 representative, from Yersinia enterocolitica subsp. enterocolitica 8081 Authors: Joachimiak, A. / Duke, N.E.C. / Feldmann, B. / Wu, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 117.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 96.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 430.1 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 42.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | authors state that the biological unit is the dimer in asymmetric unit |
-
Components
#1: Protein | Mass: 26958.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-K / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.79 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.15M potassium bromide, 30% w/v polyethylene glycol monomethyl ether 2000 (Hampton Index #96), pH 7.60, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 18, 2009 / Details: Si (111) double crystal monochromator | |||||||||
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.9→100 Å / Num. all: 755369 / Num. obs: 702493 / % possible obs: 93 % / Observed criterion σ(F): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.065 | |||||||||
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 6.4 / Rsym value: 0.248 / % possible all: 95 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.943 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→79.56 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
|