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Open data
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Basic information
Entry | Database: PDB / ID: 7r27 | ||||||
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Title | Crystal structure of the L. plantarum D-alanine ligase DltA | ||||||
![]() | D-alanine--D-alanyl carrier protein ligase | ||||||
![]() | CYTOSOLIC PROTEIN / D-alanine ligase / D-alanylation / AMP intermediate / teichoic acids | ||||||
Function / homology | ![]() D-alanine-[D-alanyl-carrier protein] ligase / D-alanine [D-alanyl carrier protein] ligase activity / lipoteichoic acid biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nikolopoulos, N. / Ravaud, S. / Simorre, J.P. / Grangeasse, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: DltC acts as an interaction hub for AcpS, DltA and DltB in the teichoic acid D-alanylation pathway of Lactiplantibacillus plantarum. Authors: Nikolopoulos, N. / Matos, R.C. / Courtin, P. / Ayala, I. / Akherraz, H. / Simorre, J.P. / Chapot-Chartier, M.P. / Leulier, F. / Ravaud, S. / Grangeasse, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177 KB | Display | ![]() |
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PDB format | ![]() | 136.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 50.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r49C ![]() 3dhvS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56141.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dltA, AYO51_00800 / Production host: ![]() ![]() References: UniProt: A0A151G8K4, D-alanine-[D-alanyl-carrier protein] ligase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, KCl |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→47.36 Å / Num. obs: 49012 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1713 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.01→2.06 Å / Rmerge(I) obs: 1.452 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3478 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DHV Resolution: 2.01→47.36 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.56 Å2 / Biso mean: 31.2965 Å2 / Biso min: 15.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.01→47.36 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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