[English] 日本語
![](img/lk-miru.gif)
- PDB-1x9h: Crystal structure of phosphoglucose/phosphomannose isomerase from... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1x9h | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum in complex with fructose 6-phosphate | ||||||
![]() | glucose-6-phosphate isomerase | ||||||
![]() | ISOMERASE / enzyme / crenarchaeon / hyperthermophile / PGI superfamily / fructose 6-phosphate | ||||||
Function / homology | ![]() mannose-6-phosphate isomerase / mannose-6-phosphate isomerase activity / carbohydrate derivative metabolic process / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / carbohydrate derivative binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C. | ||||||
![]() | ![]() Title: Structural basis for phosphomannose isomerase activity in phosphoglucose isomerase from Pyrobaculum aerophilum: a subtle difference between distantly related enzymes. Authors: Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C. #1: ![]() Title: A novel phosphoglucose isomerase/phosphomannose isomerase from the crenarchaeon Pyrobaculum aerophilum is a member of the PGI superfamily: structural evidence at 1.16 A resolution Authors: Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C. #2: ![]() Title: Crystallization and preliminary X-ray diffraction analysis of phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum Authors: Swan, M.K. / Hansen, T. / Schoenheit, P. / Davies, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 257.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 208.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1x9iC ![]() 1tzbS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit is a dimer. The asymmetric unit is a dimer. |
-
Components
#1: Protein | Mass: 33590.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 18312750, UniProt: Q8ZWV0*PLUS, glucose-6-phosphate isomerase, mannose-6-phosphate isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% polyethylene glycol 8000, 0.22M ammonium sulphate, 100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→36 Å / Num. all: 86757 / Num. obs: 86757 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.7 / Num. unique all: 7410 / Rsym value: 0.391 / % possible all: 82.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: REFINEMENT Starting model: pdb entry 1TZB Resolution: 1.5→36 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.157 / SU ML: 0.064 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.35 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
|