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- PDB-7f71: Crystal structure of the Mycobacterium tuberculosis L,D-transpept... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f71 | ||||||||||||
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Title | Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) with peptidoglycan sugar moiety and glutamate | ||||||||||||
![]() | L,D-transpeptidase 2 | ||||||||||||
![]() | HYDROLASE / L / D-transpeptidase / Cysteine protease | ||||||||||||
Function / homology | ![]() peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kumar, P. / Lamichhane, G. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Allosteric cooperation in beta-lactam binding to a non-classical transpeptidase. Authors: Ahmad, N. / Dugad, S. / Chauhan, V. / Ahmed, S. / Sharma, K. / Kachhap, S. / Zaidi, R. / Bishai, W.R. / Lamichhane, G. / Kumar, P. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332 KB | Display | ![]() |
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PDB format | ![]() | 216.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 37.9 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f8pC ![]() 5e1gS 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: 39532.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases #2: Chemical | #3: Chemical | #4: Sugar | ChemComp-BGC / | #5: 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: 2.87 Å3/Da / Density % sol: 57 % / Description: Crystal Plates |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% 5000MME, 200mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2016 / Details: mirrors |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→29.73 Å / Num. obs: 173244 / % possible obs: 96 % / Redundancy: 4.3 % / Biso Wilson estimate: 12.41 Å2 / CC1/2: 0.9 / CC star: 0.95 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.03 / Rrim(I) all: 0.067 / Rsym value: 0.048 / Χ2: 1.007 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.58→1.61 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5750 / CC1/2: 0.729 / CC star: 0.918 / Rpim(I) all: 0.306 / Rrim(I) all: 0.653 / Rsym value: 0.55 / Χ2: 0.77 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E1G Resolution: 1.58→29.73 Å / SU ML: 0.133 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3729 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→29.73 Å
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Refine LS restraints |
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LS refinement shell |
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