[English] 日本語
![](img/lk-miru.gif)
- PDB-1oj4: Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1oj4 | ||||||
---|---|---|---|---|---|---|---|
Title | Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | ||||||
![]() | 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE | ||||||
![]() | TRANSFERASE / KINASE / ISOPRENOIDS BIOSYNTHESIS / GHMP KINASE SUPERFAMILY TRANSFERASE | ||||||
Function / homology | ![]() 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase / 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Miallau, L. / Alphey, M.S. / Hunter, W.N. | ||||||
![]() | ![]() Title: Biosynthesis of Isoprenoids: Crystal Structure of 4-Diphosphocytidyl-2C-Methyl-D-Erythritol Kinase Authors: Miallau, L. / Alphey, M.S. / Kemp, L.E. / Leonard, G.A. / Mcsweeney, S.M. / Hecht, S. / Bacher, A. / Eisenreich, W. / Rohdich, F. / Hunter, W.N. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 128.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 108 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31266.721 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8FI04, 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: ATP + 4-(CYTIDINE 5'-DIPHOSPHO)-2-C -METHYL-D-ERYTHRITOL = ADP + 2-PHOSPHO-4- ...CATALYTIC ACTIVITY: ATP + 4-(CYTIDINE 5'-DIPHOSPHO)-2-C -METHYL-D-ERYTHRITOL | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20 % POLYETHYLENE GLYCOL 8000 0.2 M MAGNESUIM ACTETATE, 0.1M SODIUM CACODYLATE PH 6.5 20MM SULFOBETAIN | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2002 / Details: LENSES |
Radiation | Monochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 39761 / % possible obs: 94.3 % / Observed criterion σ(I): 5.58 / Redundancy: 2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.89 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 5.6 / % possible all: 92.3 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 364197 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 92.3 % / Rmerge(I) obs: 0.0147 / Mean I/σ(I) obs: 5.6 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER / Resolution: 2.01→65.94 Å / SU B: 3.4 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.153 Details: FURTHER REFINEMENTS SHOWED A SINGLE CONFORMATION OF THE GAMMA-PHOSHATE IN THE A-SUBUNIT
| ||||||||||||||||||||
Displacement parameters | Biso mean: 18.254 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→65.94 Å
| ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Num. reflection Rfree: 1988 / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.166 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|