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Yorodumi- PDB-2x5o: Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x5o | ||||||
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Title | Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thiazolidine-2,4-dione Inhibitors of MurD Ligase | ||||||
Components | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
Keywords | LIGASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / CELL SHAPE / CELL WALL BIOGENESIS/DEGRADATION / PEPTIDOGLYCAN SYNTHESIS | ||||||
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 division / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli DH5[alpha] (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Zidar, N. / Tomasic, T. / Sink, R. / Rupnik, V. / Kovac, A. / Turk, S. / Contreras-Martel, C. / Dessen, A. / Blanot, D. / Gobec, S. ...Zidar, N. / Tomasic, T. / Sink, R. / Rupnik, V. / Kovac, A. / Turk, S. / Contreras-Martel, C. / Dessen, A. / Blanot, D. / Gobec, S. / Zega, A. / Peterlin-Masic, L. / Kikelja, D. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2010 Title: Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase. Authors: Zidar, N. / Tomasic, T. / Sink, R. / Rupnik, V. / Kovac, A. / Turk, S. / Patin, D. / Blanot, D. / Contreras Martel, C. / Dessen, A. / Muller Premru, M. / Zega, A. / Gobec, S. / Peterlin Masic, L. / Kikelj, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x5o.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x5o.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 2x5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x5o_validation.pdf.gz | 733 KB | Display | wwPDB validaton report |
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Full document | 2x5o_full_validation.pdf.gz | 740.2 KB | Display | |
Data in XML | 2x5o_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 2x5o_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/2x5o ftp://data.pdbj.org/pub/pdb/validation_reports/x5/2x5o | HTTPS FTP |
-Related structure data
Related structure data | 2wjpC 3uagS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47157.480 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-438 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Strain: DH5[ALPHA] / Plasmid: PABD16/MURD / Production host: Escherichia coli DH5[alpha] (bacteria) References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase |
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-Non-polymers , 6 types, 544 molecules
#2: Chemical | ChemComp-VSV / | ||||||
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#3: Chemical | ChemComp-AZI / | ||||||
#4: Chemical | #5: Chemical | ChemComp-SO3 / | #6: Chemical | ChemComp-CL / #7: 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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 1.8 M (NH4)2SO4, 7% PEG 400, 100 MM NACL, 100MM HEPES, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→47.36 Å / Num. obs: 93804 / % possible obs: 86.2 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Biso Wilson estimate: 24.226 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.46→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UAG Resolution: 1.46→47.36 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.805 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→47.36 Å
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Refine LS restraints |
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