[English] 日本語
![](img/lk-miru.gif)
- PDB-4lum: The crystal structure of the P132V mutant of Pyrococcus furiosus ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4lum | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of the P132V mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese and fructose-6- phosphate. | ||||||
![]() | Glucose-6-phosphate isomerase | ||||||
![]() | ISOMERASE / Cupin Fold / Glucose 6-phosphate and Fructose 6-phosphate binding protein | ||||||
Function / homology | ![]() glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baker, P.J. / Almourfi, F.M. | ||||||
![]() | ![]() Title: Correlated mutation analysis as a tool for smart library design to improve protein performance. Authors: Baker, P.J. / Almourfi, F.M. / Raedts, J. / Joosten, H.-J. / Hendriks, S. / Kengen, S.W.M. / Hage, W.R. / Schaap, P.J. / Sedelnikova, S.E. / Van der Oost, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 171.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 136.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 773.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 776 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ltaC ![]() 4lukC ![]() 4lulC ![]() 1x7nS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetric unit contains the biological dimer. |
-
Components
#1: Protein | Mass: 21638.648 Da / Num. of mol.: 2 / Mutation: P132V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.12 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium nitrate, 0.1 M Bis Tris Propane PH6.5, 20% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2011 / Details: Diamond I03 |
Radiation | Monochromator: Diamond I03 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→18.49 Å / Num. all: 33074 / Num. obs: 33074 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 1.79→1.84 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2386 / % possible all: 94 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1X7N Resolution: 1.79→18.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.138 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.451 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 27.347 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→18.49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.794→1.84 Å / Total num. of bins used: 20
|