[English] 日本語
![](img/lk-miru.gif)
- PDB-6u1f: Thermus thermophilus D-alanine-D-alanine ligase in complex with A... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6u1f | ||||||
---|---|---|---|---|---|---|---|
Title | Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, Mg2+ and Cs+ | ||||||
![]() | D-alanine--D-alanine ligase | ||||||
![]() | LIGASE / ATP-grasp domain / ATP binding / metal binding | ||||||
Function / homology | ![]() D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pederick, J.L. / Bruning, J.B. | ||||||
![]() | ![]() Title: d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations. Authors: Pederick, J.L. / Thompson, A.P. / Bell, S.G. / Bruning, J.B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 148.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 112.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 37.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u1cC ![]() 6u1dC ![]() 6u1eC ![]() 6u1gC ![]() 6u1hC ![]() 6u1iC ![]() 6u1jC ![]() 6u1kC ![]() 2zdhS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35788.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: ddl, TTHA1587 / Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 236 molecules ![](data/chem/img/DAL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DAL / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CS / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.56 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 15-18% PEG 3350, 100 mM Bis-Tris pH 6.8, 100 mM magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→48.02 Å / Num. obs: 40323 / % possible obs: 100 % / Redundancy: 17.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.052 / Rrim(I) all: 0.225 / Net I/σ(I): 9.8 / Num. measured all: 722624 / Scaling rejects: 36 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2ZDH Resolution: 2.3→47.715 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.68 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.13 Å2 / Biso mean: 49.8073 Å2 / Biso min: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→47.715 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|