[English] 日本語
![](img/lk-miru.gif)
- PDB-7dp4: Crystal structure of wild type Brugia malayi thymidylate synthase... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7dp4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of wild type Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate and methotrexate | ||||||
![]() | Thymidylate synthase | ||||||
![]() | TRANSFERASE / THYMIDYLATE SYNTHASE / NUCLEOTIDE SYNTHASE / METHYLTRANSFERASE | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / dihydrofolate reductase activity / methylation / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Keyunratsami, K. / Nualnoi, T. / Wongkamchai, S. / Songsiriritthigul, C. / Chen, C.-J. / Canyuk, B. | ||||||
![]() | ![]() Title: Crystallographic investigation and inhibition of Brugia malayi thymidylate synthase by a folate analog Authors: Keyunratsami, K. / Nualnoi, T. / Wongkamchai, S. / Songsiriritthigul, C. / Chen, C.-J. / Canyuk, B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dp5C ![]() 7dp6C ![]() 1hvyS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34522.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Bma-tyms-1.1, BM_BM7277 / Plasmid: PQE-30 XA / Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-UMP / | ||||
#3: Chemical | ChemComp-MTX / | ||||
#4: Chemical | ChemComp-BME / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.9 % |
---|---|
Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 0.9 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2013 / Details: DCM |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 65291 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Net I/σ(I): 26.06 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.16 / Num. unique obs: 6480 / CC1/2: 0.718 / CC star: 0.914 / Rpim(I) all: 0.331 / Rrim(I) all: 0.597 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1HVY Resolution: 1.5→25.855 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.213 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.061 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.565 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→25.855 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|