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Yorodumi- PDB-2y1o: Dual-target Inhibitor of MurD and MurE Ligases: Design, Synthesis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y1o | ||||||
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Title | Dual-target Inhibitor of MurD and MurE Ligases: Design, Synthesis and Binding Mode Studies | ||||||
Components | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
Keywords | LIGASE / CELL CYCLE / CELL DIVISION / CELL SHAPE / CELL WALL BIOGENESIS/DEGRADATION | ||||||
Function / homology | Function and homology information UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Tomasic, T. / Sink, R. / Kovac, A. / Turk, S. / Contreras-Martel, C. / Dessen, A. / Blanot, D. / Gobec, S. / Zega, A. / Kikelj, D. / Peterlin-Masic, L. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2012 Title: Dual Inhibitor of MurD and MurE Ligases from Escherichia coli and Staphylococcus aureus. Authors: Tomasic, T. / Sink, R. / Zidar, N. / Fic, A. / Contreras-Martel, C. / Dessen, A. / Patin, D. / Blanot, D. / Muller-Premru, M. / Gobec, S. / Zega, A. / Kikelj, D. / Masic, L.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y1o.cif.gz | 194.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y1o.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 2y1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/2y1o ftp://data.pdbj.org/pub/pdb/validation_reports/y1/2y1o | HTTPS FTP |
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-Related structure data
Related structure data | 1uagS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47979.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DH5[ALPHA] / Plasmid: PABD16/MURD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase | ||||
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#2: Chemical | ChemComp-T26 / ( | ||||
#3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.9 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 6.0 MG/ML MURD, 20 MM HEPES, PH 7.4, 200 MM NACL, 5 MM DITHIOTHREITOL, 0.05% (W/V) NAN3 0.1. M HEPES PH 7.5, 1.9 M AMMONIUM SULPHATE, 7% (W/V) PEG 400, 50 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97238 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97238 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→46.56 Å / Num. obs: 91441 / % possible obs: 82.8 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 25.693 Å2 / Rsym value: 0.04 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.49→1.58 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.47 / % possible all: 52.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UAG Resolution: 1.49→46.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.149 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.543 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→46.56 Å
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Refine LS restraints |
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