[English] 日本語
![](img/lk-miru.gif)
- PDB-3he3: Crystal Structure of UDP-galactopyranose mutase in complex with UDP -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3he3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of UDP-galactopyranose mutase in complex with UDP | ||||||
![]() | UDP-galactopyranose mutase | ||||||
![]() | ISOMERASE / UDP-galactopyranose mutase / inhibitor / UDP | ||||||
Function / homology | ![]() UDP-galactopyranose mutase activity / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Partha, S.K. / van Straaten, K.E. / Sanders, D.A.R. | ||||||
![]() | ![]() Title: Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP. Authors: Partha, S.K. / van Straaten, K.E. / Sanders, D.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 771.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 636.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3hdqC ![]() 3hdyC ![]() 1v0jS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 45741.824 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: R1 / Gene: DR_A0367 / Plasmid: pEHISTEV / Production host: ![]() ![]() #2: Chemical | ChemComp-UDP / #3: Chemical | ChemComp-FAD / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.42 % |
---|---|
Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.5 Details: 0.1 M HEPES, 0.2 M LiCl and 28% PEG 6000, pH 6.5, Microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2009 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39.88 Å / Num. obs: 204114 / % possible obs: 98.9 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.182 / Rsym value: 0.182 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.5 / Num. unique all: 66447 / Rsym value: 0.598 / % possible all: 93.1 |
-
Processing
Software | Name: PHENIX / Version: (phenix.refine) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1V0J Resolution: 2.4→39.88 Å / SU ML: -0 / σ(F): 1.34 / Phase error: 28.8 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.776 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.88 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|