[English] 日本語
![](img/lk-miru.gif)
- PDB-1bu6: CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MU... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1bu6 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION | ||||||
![]() | PROTEIN (GLYCEROL KINASE) | ||||||
![]() | TRANSFERASE / ALLOSTERY / COOPERATIVITY / GLYCEROL KINASE | ||||||
Function / homology | ![]() glycerol-3-phosphate metabolic process / glycerol kinase / glycerol kinase activity / glycerol metabolic process / glycerol catabolic process / DNA damage response / zinc ion binding / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Feese, M.D. / Faber, H.R. / Bystrom, C.E. / Pettigrew, D.W. / Remington, S.J. | ||||||
![]() | ![]() Title: Glycerol kinase from Escherichia coli and an Ala65-->Thr mutant: the crystal structures reveal conformational changes with implications for allosteric regulation. Authors: Feese, M.D. / Faber, H.R. / Bystrom, C.E. / Pettigrew, D.W. / Remington, S.J. #1: ![]() Title: A Single Amino Acid Change in Escherichia Coli Glycerol Kinase Abolishes Glucose Control of Glycerol Utilization in Vivo Authors: Pettigrew, D.W. / Liu, W.Z. / Holmes, C. / Meadow, N.D. / Roseman, S. #2: ![]() Title: Cation Promoted Association (Cpa) of a Regulatory and Target Protein is Controlled by Protein Phosphorylation Authors: Feese, M.D. / Pettigrew, D.W. / Meadow, N.D. / Roseman, S. / Remington, S.J. #3: ![]() Title: Escherichia Coli Glycerol Kinase: Role of a Tetramer Interface in Regulation by Fructose-1,6-Bisphosphate and Phosphotransferase System Regulatory Protein Iiiglc Authors: Liu, W.Z. / Faber, H.R. / Feese, M.D. / Remington, S.J. / Pettigrew, D.W. #4: ![]() Title: Structure of the Regulatory Complex of Escherichia Coli III==Glc== with Glycerol Kinase Authors: Hurley, J.H. / Faber, H.R. / Worthylake, D. / Meadow, N.D. / Roseman, S. / Pettigrew, D.W. / Remington, S.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 394.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 320 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1glfSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 56192.379 Da / Num. of mol.: 4 / Mutation: A65T Source method: isolated from a genetically manipulated source Details: GLYCEROL SULPHATE / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20-22% (W/V) POLYETHYLENE GLYCOL MR 4000 0.2 M LISO4 0.1 M TRIS PH 8.5 - 8.8 CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION AT ROOM TEMPERATURE., vapor diffusion - hanging drop PH range: 8.5-8.8 / Temp details: room temp | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Faber, H.R., (1989) J. Mol. Biol., 207, 637. / PH range low: 7 / PH range high: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Aug 15, 1994 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→20 Å / Num. obs: 69682 / % possible obs: 74 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.068 |
Reflection | *PLUS Lowest resolution: 37 Å / % possible obs: 74 % / Num. measured all: 132331 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1GLF Resolution: 2.37→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: BSOL AND KSOL SET BY USER GLYCEROL KINASE EXISTS AT PHYSIOLOGICAL CONCENTRATIONS IN AN EQUILIBRIUM BETWEEN FUNCTIONAL DIMERS AND TETRAMERS. THE CRYSTAL ASYMMETRIC UNIT CONTAINS A TETRAMER OF ...Details: BSOL AND KSOL SET BY USER GLYCEROL KINASE EXISTS AT PHYSIOLOGICAL CONCENTRATIONS IN AN EQUILIBRIUM BETWEEN FUNCTIONAL DIMERS AND TETRAMERS. THE CRYSTAL ASYMMETRIC UNIT CONTAINS A TETRAMER OF GLYCEROL KINASE WITH NEARLY EXACT 222 POINT-GROUP SYMMETRY, UNLIKE THE PREVIOUSLY SUBMITTED GLYCEROL KINASE - FACTOR IIIGLC COMPLEX IN WHICH THE 222 POINT GROUP SYMMETRY WAS CRYSTALLOGRAPHICALLY ENFORCED
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: TNT SOLVENT MODELING / Bsol: 300 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5F-6 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|