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Yorodumi- PDB-3vyp: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vyp | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2-N140 adduct with meropenem | ||||||
Components | Probable conserved lipoprotein LPPS | ||||||
Keywords | TRANSFERASE / BETA BARREL / YkuD domain / L / D-transpeptidase / beta-lactam binding | ||||||
Function / homology | Function and homology information peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region ...peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Li, W.J. / Li, D.F. / Bi, L.J. / Wang, D.C. | ||||||
Citation | Journal: Cell Res. / Year: 2013 Title: Crystal structure of L,D-transpeptidase LdtMt2 in complex with meropenem reveals the mechanism of carbapenem against Mycobacterium tuberculosis Authors: Li, W.J. / Li, D.F. / Hu, Y.L. / Zhang, X.E. / Bi, L.J. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vyp.cif.gz | 240.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vyp.ent.gz | 191.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vyp_validation.pdf.gz | 1008.6 KB | Display | wwPDB validaton report |
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Full document | 3vyp_full_validation.pdf.gz | 1013.8 KB | Display | |
Data in XML | 3vyp_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 3vyp_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vyp ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vyp | HTTPS FTP |
-Related structure data
Related structure data | 3vynC 3vyoSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29280.438 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, residues 140-408 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2518c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: O53223, UniProt: I6Y9J2*PLUS, EC: 2.3.2.12 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M ammonium acetate, 0.1M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→36.42 Å / Num. all: 101851 / Num. obs: 101442 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 1.9 / Num. unique all: 14388 / Rsym value: 0.535 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VYO Resolution: 1.4→35.864 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.8724 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 84.246 Å2 / ksol: 0.423 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 238.25 Å2 / Biso mean: 23.9095 Å2 / Biso min: 8.26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→35.864 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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