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Yorodumi- PDB-7b6i: Crystal structure of MurE from E.coli in complex with Z1373445602 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b6i | ||||||
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Title | Crystal structure of MurE from E.coli in complex with Z1373445602 | ||||||
Components | UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2 / 6-diaminopimelate ligase cell wall biosynthesis ligase drug target / Structural Genomics / Structural Genomics Consortium / SGC / fragment screening | ||||||
Function / homology | Function and homology information UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.069 Å | ||||||
Authors | Koekemoer, L. / Steindel, M. / Fairhead, M. / Talon, R. / Douangamath, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of MurE from E.coli Authors: Koekemoer, L. / Steindel, M. / Fairhead, M. / Talon, R. / Douangamath, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b6i.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b6i.ent.gz | 156.3 KB | Display | PDB format |
PDBx/mmJSON format | 7b6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/7b6i ftp://data.pdbj.org/pub/pdb/validation_reports/b6/7b6i | HTTPS FTP |
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-Related structure data
Related structure data | 7b53SC 7b60C 7b61C 7b68C 7b6gC 7b6jC 7b6kC 7b6lC 7b6mC 7b6nC 7b6oC 7b6pC 7b6qC 7b9eC 7b9wC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 53493.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: murE, b0085, JW0083 / Plasmid: pNIC28-Bsa4 Details (production host): N-terminal His6-tag -Twin-Strep-tag II -TEV-cleavage site Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): -R3-Rosetta References: UniProt: P22188, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase #2: Chemical | ChemComp-CIT / | #3: Chemical | ChemComp-SZE / | #4: Chemical | ChemComp-IPA / | #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: 2.26 Å3/Da / Density % sol: 45.58 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 19% PEG4K 14% 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→73.51 Å / Num. obs: 56353 / % possible obs: 91.6 % / Redundancy: 1.8 % / CC1/2: 0.998 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.02→2.13 Å / Num. unique obs: 7369 / CC1/2: 0.424 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7B53 Resolution: 2.069→73.51 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.642 / SU ML: 0.192 / Cross valid method: FREE R-VALUE / ESU R: 0.256 / ESU R Free: 0.21 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.926 Å2
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Refinement step | Cycle: LAST / Resolution: 2.069→73.51 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: 20
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