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- PDB-5e51: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5.0E+51 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 1 with Faropenem adduct | ||||||
![]() | L,D-transpeptidase 1 | ||||||
![]() | TRANSFERASE / L / D-transpeptidase 1 / Peptidoglycan synthesis enzyme / cell wall enzyme / ldtMt1 / Mycobacterium tuberculosis | ||||||
Function / homology | ![]() peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / periplasmic space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, P. / Lamichhane, G. / Ginell, S.L. | ||||||
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 | ![]() | 159 KB | Display | ![]() |
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PDB format | ![]() | 123.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471 KB | Display | ![]() |
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Full document | ![]() | 487.9 KB | Display | |
Data in XML | ![]() | 31.2 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5du7C ![]() 5dujC ![]() 5dvpC ![]() 5dzjC ![]() 5dzpC ![]() 5e1gC ![]() 5e1iC ![]() 5e5lC ![]() 5k69C ![]() 4jmnS 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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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23966.965 Da / Num. of mol.: 4 / Fragment: UNP residues 32-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CDC 1551 / Oshkosh / Gene: ldtA, MT0125 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: Q7DAG3, UniProt: O53638*PLUS, Transferases; Acyltransferases; Aminoacyltransferases #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | Faropenem upon beta-lactam ring opening and aceylation to enzyme undergoes a further cleavage with ...Faropenem upon beta-lactam ring opening and aceylation to enzyme undergoes a further cleavage with a small peace of drug (R2 group) remaining attached to the enzyme as Faropenem adduct (5KO) in the structure. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG6000, Bicine / PH range: pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2015 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.5 |
Reflection | Resolution: 2.25→19.878 Å / Num. obs: 81604 / % possible obs: 87.85 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.265 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JMN Resolution: 2.25→19.878 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.21 / Stereochemistry target values: TWIN_LSQ_F
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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: 2.25→19.878 Å
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Refine LS restraints |
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LS refinement shell |
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