[English] 日本語
![](img/lk-miru.gif)
- PDB-7fgq: Crystal structure of Thymidylate kinase with TMP and its low-reso... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7fgq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Thymidylate kinase with TMP and its low-resolution (SAXS) solution structure from Brugia malayi | ||||||
![]() | dTMP kinase | ||||||
![]() | TRANSFERASE / Thymidylate Kinase / Nucleotide biosynthesis / ATP binding / Nucleotide binding / Complexed with dTMP | ||||||
Function / homology | ![]() dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramachandran, R. / Vishwakarma, J. / Sharma, V.K. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structure of Thymidylate kinase with TMP and its low-resolution (SAXS) solution structure from Brugia malayi Authors: Ramachandran, R. / Vishwakarma, J. / Sharma, V.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 56.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 37.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 779.6 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e9cS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28412.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Bm5401, Bm1_23075, BM_Bm5401 / Plasmid: pET28a / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-TMP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.09 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: Diammonium tartrate, Bis-Tris pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→41.881 Å / Num. obs: 16977 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Χ2: 0.94 / Net I/av σ(I): 16.2 / Net I/σ(I): 2.2 |
Reflection shell | Resolution: 1.91→8.96 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.107 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 16977 / CC1/2: 0.741 / Rpim(I) all: 0.504 / Χ2: 0.94 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1e9c Resolution: 1.91→41.881 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.1 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→41.881 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|