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Open data
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Basic information
Entry | Database: PDB / ID: 3h46 | ||||||
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Title | Glycerol Kinase H232E with Glycerol | ||||||
![]() | Glycerol kinase | ||||||
![]() | TRANSFERASE / glycerol / 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.8 KB | Display | ![]() |
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PDB format | ![]() | 161.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.4 KB | Display | ![]() |
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Full document | ![]() | 494.7 KB | Display | |
Data in XML | ![]() | 39.3 KB | Display | |
Data in CIF | ![]() | 54.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3d7eC ![]() 3flcC ![]() 3h3nC ![]() 3h3oC ![]() 3h45C ![]() 1xupS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55803.453 Da / Num. of mol.: 2 / Mutation: H232E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: HEPES, PEG 550 MME, ZnSO4, pH 6.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 100197 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rsym value: 0.096 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.75→1.86 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.509 / % possible all: 81.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XUP Resolution: 1.75→10 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 3 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Displacement parameters | Biso max: 66.45 Å2 / Biso mean: 25.631 Å2 / Biso min: 10.72 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→10 Å
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LS refinement shell | Resolution: 1.751→1.795 Å / Total num. of bins used: 20
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