[English] 日本語
![](img/lk-miru.gif)
- PDB-7n9d: I74A mutant of the isopentenyl phosphate kinase from Candidatus m... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7n9d | ||||||
---|---|---|---|---|---|---|---|
Title | I74A mutant of the isopentenyl phosphate kinase from Candidatus methanomethylophilus alvus | ||||||
![]() | Isopentenyl phosphate kinase | ||||||
![]() | TRANSFERASE / Phosphotransferase ATP Biocatalysis Isoprenoids Enzyme Promiscuity | ||||||
Function / homology | ![]() isopentenyl phosphate kinase / isopentenyl phosphate kinase activity / glutamate 5-kinase activity / proline biosynthetic process / isoprenoid biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thomas, L.M. / Singh, S. / Johnson, B.P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus . Authors: Johnson, B.P. / Kumar, V. / Scull, E.M. / Thomas, L.M. / Bourne, C.R. / Singh, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 145.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lntC ![]() 7lnuC ![]() 7lnvSC ![]() 7lnwC ![]() 7lnxC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 30491.146 Da / Num. of mol.: 2 / Mutation: I74A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BKD89_07040 / Production host: ![]() ![]() References: UniProt: A0A3G3II74, isopentenyl phosphate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.87 % |
---|---|
Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5 M Sodium Formate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 24, 2021 / Details: Osmic Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35 Å / Num. obs: 41416 / % possible obs: 99.4 % / Redundancy: 10.8 % / Biso Wilson estimate: 29.46 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 12.32 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 1.189 / Num. unique obs: 1983 / CC1/2: 0.662 / Rsym value: 0.745 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7LNV Resolution: 2.1→27.06 Å / SU ML: 0.2916 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4912 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→27.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|