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- PDB-4qtf: Structure and specificity of L-D-Transpeptidase from Mycobacteriu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qtf | ||||||
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Title | Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation | ||||||
![]() | L,d-transpeptidase LdtB | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Structural Genomics / Enzyme Function Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / L-D-transpeptidase / D-D-transpeptidase / imipenem / meropenem / peptidoglycan / beta-lactamase / cross-linkage / HYDROLASE-HYDROLASE 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 | ![]() ![]() ![]() | ||||||
![]() | Gokulan, K. / Varughese, K.I. | ||||||
![]() | ![]() Title: Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation Authors: Gokulan, K. / Khare, S. / Cerniglia, C.E. / Foley, S.L. / Varughese, K.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.7 KB | Display | ![]() |
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PDB format | ![]() | 116.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4qr7SC ![]() 4qraC ![]() 4qrbC 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37381.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MLD / |
#3: Chemical | ChemComp-3V5 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.03 M citric acid, 0.07 M BIS-TRIS propane pH 7.6 and 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K PH range: 7,6 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR-325 CCD detector / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.3 Å / Num. obs: 25603 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QR7 Resolution: 2→42.35 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.918 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 37.447 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.35 Å
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Refine LS restraints |
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