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Yorodumi- PDB-5uwv: Crystal structure of Mycobacterium abscessus L,D-transpeptidase 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uwv | ||||||
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Title | Crystal structure of Mycobacterium abscessus L,D-transpeptidase 2 | ||||||
Components | L,D-TRANSPEPTIDASE 2 | ||||||
Keywords | TRANSFERASE / L / D-transpeptidase / Peptidoglycan synthesis enzyme / cell wall enzyme / LdtMab2 / Mycobacterium abscessus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium abscessus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å | ||||||
Authors | Kumar, P. / Ginell, S.L. / Lamichhane, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Antimicrob. Agents Chemother. / Year: 2017 Title: Mycobacterium abscessus l,d-Transpeptidases Are Susceptible to Inactivation by Carbapenems and Cephalosporins but Not Penicillins. Authors: Kumar, P. / Chauhan, V. / Silva, J.R.A. / Lameira, J. / d'Andrea, F.B. / Li, S.G. / Ginell, S.L. / Freundlich, J.S. / Alves, C.N. / Bailey, S. / Cohen, K.A. / Lamichhane, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uwv.cif.gz | 378.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uwv.ent.gz | 308.2 KB | Display | PDB format |
PDBx/mmJSON format | 5uwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uwv_validation.pdf.gz | 476.8 KB | Display | wwPDB validaton report |
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Full document | 5uwv_full_validation.pdf.gz | 496 KB | Display | |
Data in XML | 5uwv_validation.xml.gz | 65.9 KB | Display | |
Data in CIF | 5uwv_validation.cif.gz | 91.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/5uwv ftp://data.pdbj.org/pub/pdb/validation_reports/uw/5uwv | HTTPS FTP |
-Related structure data
Related structure data | 5du7S 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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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 39522.059 Da / Num. of mol.: 6 / Fragment: UNP residues 42-406 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria) Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 Gene: MAB_1530 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1MMQ4 #2: 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: 3.53 Å3/Da / Density % sol: 65.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 13% PEG 8000, 110 mM sodium citrate tribasic dihydrate PH range: pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2015 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→135.53 Å / Num. obs: 65870 / % possible obs: 99.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 56.54 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.02 |
Reflection shell | Resolution: 2.98→3.087 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.52 / Num. unique obs: 5838 / CC1/2: 0.78 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DU7 Resolution: 2.98→135.53 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.874 / SU B: 18.041 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.565 / ESU R Free: 0.409 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.68 Å2 / Biso mean: 58.908 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 2.98→135.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.981→3.058 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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