[English] 日本語
![](img/lk-miru.gif)
- PDB-6kdu: Structural basis for domain rotation during adenylation of active... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6kdu | ||||||
---|---|---|---|---|---|---|---|
Title | Structural basis for domain rotation during adenylation of active site K123 and fragment library screening against NAD+ -dependent DNA ligase from Mycobacterium tuberculosis | ||||||
![]() | DNA ligase A | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramachandran, R. / Shukla, A. / Afsar, M. | ||||||
![]() | ![]() Title: Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are important for the initial ...Title: Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity. Authors: Afsar, M. / Shukla, A. / Kumar, N. / Ramachandran, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 134.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 103.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6krhC ![]() 6kscC ![]() 6ksdC ![]() 1zauS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | |
Other databases |
|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 36846.125 Da / Num. of mol.: 1 / Mutation: E22A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: H37Rv / Gene: ligA / Plasmid: pQE60 Production host: ![]() ![]() ![]() References: UniProt: P9WNV1, ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-AMP / ![]() | ||||
#3: Chemical | ChemComp-NMN / ![]() | ||||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.25 % |
---|---|
Crystal grow![]() | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.1M HEPES Na pH=7.6 0.1M NaCl 1.5 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo conditions / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 14, 2019 / Details: Cilindrical Mirror with 50 nm Pt-coating | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si111 with LN2 closed loop cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→48.084 Å / Num. obs: 28776 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.017 / Rrim(I) all: 0.074 / Net I/σ(I): 32.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 1ZAU Resolution: 2.2→48.084 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.11
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.66 Å2 / Biso mean: 48.723 Å2 / Biso min: 18.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→48.084 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
|