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- PDB-5k69: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k69 | |||||||||
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Title | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T224 | |||||||||
![]() | L,D-transpeptidase 2 | |||||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / peptidase / IgD_like domain / YkuD domain / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Lamichhane, G. / Ginell, S.L. / Kumar, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Non-classical transpeptidases yield insight into new antibacterials. Authors: Kumar, P. / Kaushik, A. / Lloyd, E.P. / Li, S.G. / Mattoo, R. / Ammerman, N.C. / Bell, D.T. / Perryman, A.L. / Zandi, T.A. / Ekins, S. / Ginell, S.L. / Townsend, C.A. / Freundlich, J.S. / Lamichhane, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.4 KB | Display | ![]() |
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PDB format | ![]() | 119.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5du7SC ![]() 5dujC ![]() 5dvpC ![]() 5dzjC ![]() 5dzpC ![]() 5e1gC ![]() 5e1iC ![]() 5e51C ![]() 5e5lC 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43407.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pET38a / Production host: ![]() ![]() References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG5000MME, Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.98 Å / Num. obs: 70044 / % possible obs: 97.8 % / Redundancy: 3.4 % / CC1/2: 0.899 / Rmerge(I) obs: 0.073 / Rsym value: 0.066 / Net I/σ(I): 14.42 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.63 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DU7 Resolution: 2.001→28.98 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→28.98 Å
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Refine LS restraints |
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LS refinement shell |
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