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Open data
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Basic information
Entry | Database: PDB / ID: 7a0z | ||||||
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Title | LppS with covalent adduct derived from 1b | ||||||
![]() | L,D-transpeptidase 2 | ||||||
![]() | LIGASE / Transpeptidase / cell wall / peptidoglycan / antibiotic / Beta-lactam / Covalent inhibitor / Mycobacterium tuberculosis | ||||||
Function / homology | ![]() peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schnell, R. / Steiner, E.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: N-Thio-beta-lactams targeting L,D-transpeptidase-2, with activity against drug-resistant strains of Mycobacterium tuberculosis. Authors: Martelli, G. / Pessatti, T.B. / Steiner, E.M. / Cirillo, M. / Caso, C. / Bisognin, F. / Landreh, M. / Monte, P.D. / Giacomini, D. / Schnell, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.2 KB | Display | ![]() |
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PDB format | ![]() | 97.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7a10C ![]() 7a11C ![]() 7a1cC ![]() 7a1eC ![]() 5lbgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 28508.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The construct used here contains two domains: domain-B (Ig-like) and domain-C (catalytic transpeptidase domain), residue range 149-408 of the full length protein. Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Production host: ![]() ![]() References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases #2: Chemical | #3: Chemical | ChemComp-TAM / | #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 | Density Matthews: 2.11 Å3/Da / Density % sol: 41.66 % / Description: rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.25 Details: Well solution: 0.1 M Na-Citrate pH 4.25 / 17.5% PEG 6K The crystals were cryo-protected by dipping them in mother liquor with increased: 25% PEG 6K |
-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: May 24, 2019 / Details: mirrors (VFM,HFM) |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94644 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→40.04 Å / Num. obs: 80547 / % possible obs: 97.1 % / Observed criterion σ(I): 1.8 / Redundancy: 3.3 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.031 / Rrim(I) all: 0.045 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3076 / CC1/2: 0.664 / Rpim(I) all: 0.39 / % possible all: 75.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LBG Resolution: 1.45→40 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.38 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.82 Å2 / Biso mean: 22.392 Å2 / Biso min: 12.69 Å2
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Refinement step | Cycle: final / Resolution: 1.45→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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