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Yorodumi- PDB-2xpc: Second-generation sulfonamide inhibitors of MurD: Activity optimi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xpc | ||||||
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Title | Second-generation sulfonamide inhibitors of MurD: Activity optimisation with conformationally rigid analogues of D-glutamic acid | ||||||
Components | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
Keywords | LIGASE / CELL CYCLE / CELL DIVISION / CELL SHAPE / CELL WALL BIOGENESIS/DEGRADATION / LIGASE SYNTHESIS | ||||||
Function / homology | Function and homology information UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / cell cycle / 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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Sosic, I. / Barreteau, H. / Simcic, M. / Sink, R. / Cesar, J. / Golic-Grdadolnik, S. / Contreras-Martel, C. / Dessen, A. / Amoroso, A. / Joris, B. ...Sosic, I. / Barreteau, H. / Simcic, M. / Sink, R. / Cesar, J. / Golic-Grdadolnik, S. / Contreras-Martel, C. / Dessen, A. / Amoroso, A. / Joris, B. / Blanot, D. / Gobec, S. | ||||||
Citation | Journal: Eur.J.Med.Chem / Year: 2011 Title: Second-Generation Sulfonamide Inhibitors of D- Glutamic Acid-Adding Enzyme: Activity Optimisation with Conformationally Rigid Analogues of D- Glutamic Acid. Authors: Sosi, I. / Barreteau, H. / Sim, M. / Sink, R. / Cesar, J. / Zega, A. / Grdadolnik, S.G. / Contreras-Martel, C. / Dessen, A. / Amoroso, A. / Joris, B. / Blanot, D. / Gobec, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xpc.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xpc.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xpc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/2xpc ftp://data.pdbj.org/pub/pdb/validation_reports/xp/2xpc | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47157.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cell line: DH5A / Plasmid: PABD16/MURD / Production host: Escherichia coli DH5[alpha] (bacteria) References: UniProt: Q8X9Y9, UniProt: P14900*PLUS, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase |
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-Non-polymers , 5 types, 496 molecules
#2: Chemical | ChemComp-051 / ( | ||||||
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#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / | #6: 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: 3.05 Å3/Da / Density % sol: 59.61 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 1.9M (NH4)2SO4,7% PEG 400, 50MM NACL, 100MM HEPES, PH 7.5 |
-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→46.43 Å / Num. obs: 91001 / % possible obs: 91.2 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Biso Wilson estimate: 26.667 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.49→1.58 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.09 / % possible all: 69.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UAG Resolution: 1.49→46.43 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.703 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 23.923 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→46.43 Å
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Refine LS restraints |
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