[English] 日本語
Yorodumi- PDB-3vyn: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vyn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2 N55 truncation mutant (resideus 55-408) | ||||||
Components | Probable conserved lipoprotein LPPS | ||||||
Keywords | TRANSFERASE / BETA BARREL / YkuD domain / L / D-transpeptidase / beta-lactam binding | ||||||
Function / homology | Function and homology information peptidoglycan-protein cross-linking / peptidoglycan-based cell wall biogenesis / peptidoglycan L,D-transpeptidase activity / peptidoglycan metabolic process / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape ...peptidoglycan-protein cross-linking / peptidoglycan-based cell wall biogenesis / peptidoglycan L,D-transpeptidase activity / peptidoglycan metabolic process / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / 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: 2.5 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vyn.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vyn.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vyn_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3vyn_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 3vyn_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 3vyn_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/3vyn ftp://data.pdbj.org/pub/pdb/validation_reports/vy/3vyn | HTTPS FTP |
-Related structure data
Related structure data | 3vyoSC 3vypC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38066.195 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, residue 55-408 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.36 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM Bis-Tis, 200mM MgCl2, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 98 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.96422 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96422 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→51.03 Å / Num. all: 29344 / Num. obs: 29308 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4207 / Rsym value: 0.497 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VYO Resolution: 2.5→48.64 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.25 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→48.64 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å
|