[English] 日本語
![](img/lk-miru.gif)
- PDB-6noq: Xanthomonas citri Phospho-PGM in complex with mannose-1-phosphate -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6noq | ||||||
---|---|---|---|---|---|---|---|
Title | Xanthomonas citri Phospho-PGM in complex with mannose-1-phosphate | ||||||
![]() | Phosphoglucomutase | ||||||
![]() | ISOMERASE / phosphoglucomutase | ||||||
Function / homology | ![]() intramolecular phosphotransferase activity / carbohydrate metabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stiers, K.M. / Beamer, L.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural and dynamical description of the enzymatic reaction of a phosphohexomutase. Authors: Stiers, K.M. / Graham, A.C. / Zhu, J.S. / Jakeman, D.L. / Nix, J.C. / Beamer, L.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 194.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 155.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 606 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 607.9 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nn1C ![]() 6nn2C ![]() 6nnnC ![]() 6nnoC ![]() 6nnpC ![]() 6nnsC ![]() 6nntC ![]() 6nnuC ![]() 6nolC ![]() 6np8C ![]() 6npxC ![]() 6nqeC ![]() 6nqfC ![]() 6nqgC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 51431.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 306 / Gene: xanA, XAC3579 / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Sugar | ChemComp-M1P / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.01 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 22% PEG 8000, 0.2M MgCl, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jan 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→46.253 Å / Num. obs: 55020 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.311 / Rpim(I) all: 0.092 / Rrim(I) all: 0.324 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.61→1.64 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.784 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2656 / CC1/2: 0.348 / Rpim(I) all: 0.652 / Rrim(I) all: 1.904 / % possible all: 99.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.61→46.253 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 27.53
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→46.253 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|