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Yorodumi- PDB-7f71: Crystal structure of the Mycobacterium tuberculosis L,D-transpept... -
+Open data
-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 | ||||||||||||
Components | L,D-transpeptidase 2 | ||||||||||||
Keywords | HYDROLASE / L / D-transpeptidase / Cysteine protease | ||||||||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||||||||
Authors | Kumar, P. / Lamichhane, G. | ||||||||||||
Funding support | India, United States, 3items
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Citation | Journal: Elife / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f71.cif.gz | 332 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f71.ent.gz | 216.2 KB | Display | PDB format |
PDBx/mmJSON format | 7f71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/7f71 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/7f71 | HTTPS FTP |
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-Related structure data
Related structure data | 7f8pC 5e1gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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