[English] 日本語
![](img/lk-miru.gif)
- PDB-5zvx: Crystal structure of K86A mutant of phosphomannose isomerase from... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5zvx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of K86A mutant of phosphomannose isomerase from Salmonella typhimurium | ||||||
![]() | Mannose-6-phosphate isomerase | ||||||
![]() | ISOMERASE / zinc binding / SUGAR BINDING PROTEIN | ||||||
Function / homology | ![]() mannose-6-phosphate isomerase / mannose-6-phosphate isomerase activity / GDP-mannose biosynthetic process / carbohydrate metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bangera, M. / Murthy, M.R.N. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural and functional insights into phosphomannose isomerase: the role of zinc and catalytic residues. Authors: Bangera, M. / Gowda K, G. / Sagurthi, S.R. / Murthy, M.R.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 104.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 452.2 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zt4C ![]() 5zt5C ![]() 5zt6C ![]() 5zuwC ![]() 5zuyC ![]() 5zv0C ![]() 5zvrC ![]() 5zvuC ![]() 3h1mS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 42732.586 Da / Num. of mol.: 1 / Mutation: K86A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: manA, pmi, STM1467 / Production host: ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.71 % |
---|---|
Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6.8 Details: 0.1 M Magnesium acetate tetrahydrate, 0.2 M Sodium cacodylate pH 6.8, 20% PEG 8000,5% dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30.58 Å / Num. obs: 43702 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rsym value: 0.09 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Rsym value: 0.55 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3H1M Resolution: 1.7→30.58 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.23 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.103 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.016 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→30.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|