+
Open data
-
Basic information
Entry | Database: PDB / ID: 3h45 | ||||||
---|---|---|---|---|---|---|---|
Title | Glycerol Kinase H232E with Ethylene Glycol | ||||||
![]() | Glycerol kinase | ||||||
![]() | TRANSFERASE / ethylene glycol / kinase / ATP-binding / Glycerol metabolism / Nucleotide-binding / Phosphoprotein | ||||||
Function / homology | ![]() glycerol kinase / glycerol-3-phosphate biosynthetic process / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / triglyceride metabolic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yeh, J.I. / Kettering, R.D. | ||||||
![]() | ![]() Title: Structural characterizations of glycerol kinase: unraveling phosphorylation-induced long-range activation Authors: Yeh, J.I. / Kettering, R. / Saxl, R. / Bourand, A. / Darbon, E. / Joly, N. / Briozzo, P. / Deutscher, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 389.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 317.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 549.7 KB | Display | |
Data in XML | ![]() | 77.8 KB | Display | |
Data in CIF | ![]() | 103.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3d7eC ![]() 3flcC ![]() 3h3nC ![]() 3h3oC ![]() 3h46C ![]() 1xupS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 55803.453 Da / Num. of mol.: 4 / Mutation: H232E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: KH2PO4, PEG 8000, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU AFC11-KAPPA / Detector: DIFFRACTOMETER / Date: Jun 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 73411 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.09 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.368 / % possible all: 99.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XUP Resolution: 2.65→12 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 3 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
| ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.87 Å2 / Biso mean: 40.25 Å2 / Biso min: 8.47 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→12 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
|