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Yorodumi- PDB-2jff: Crystal structure of MurD ligase in complex with D-Glu containing... -
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-Basic information
Entry | Database: PDB / ID: 2jff | ||||||
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Title | Crystal structure of MurD ligase in complex with D-Glu containing sulfonamide inhibitor | ||||||
Components | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
Keywords | LIGASE / MURD-INHIBITOR COMPLEX / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / CELL SHAPE / CELL CYCLE / NUCLEOTIDE-BINDING / SULFONAMIDE INHIBITOR / MURD LIGASE / ATP-BINDING / CELL DIVISION | ||||||
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: 1.89 Å | ||||||
Authors | Kotnik, M. / Humljan, J. / Contreras-Martel, C. / Oblak, M. / Kristan, K. / Herve, M. / Blanot, D. / Urleb, U. / Gobec, S. / Dessen, A. / Solmajer, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural and Functional Characterization of Enantiomeric Glutamic Acid Derivatives as Potential Transition State Analogue Inhibitors of Murd Ligase. Authors: Kotnik, M. / Humljan, J. / Contreras-Martel, C. / Oblak, M. / Kristan, K. / Herve, M. / Blanot, D. / Urleb, U. / Gobec, S. / Dessen, A. / Solmajer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jff.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jff.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/2jff ftp://data.pdbj.org/pub/pdb/validation_reports/jf/2jff | HTTPS FTP |
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-Related structure data
Related structure data | 2jfgC 2jfhC 3uagS 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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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 Details: INHIBITOR N-(6-BUTOXY-NAPHTHALENE-2-SULFONYL)-D-GLUTAMIC ACID BOUND Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PABD16 / Production host: Escherichia coli DH5[alpha] (bacteria) References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase | ||||
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#2: Chemical | ChemComp-LK2 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | C-TERMINAL HIS-TAG (SHHHHHH) | |
-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: BOTH LIGANDS (UMA AND ADP), AS WELL AS THE SIDE-CHAINS OF AMINO ACID RESIDUES WITHIN THE SUBSTRATE BINDING SITES AND ALSO KCX198 WERE DELETED TO AVOID BIAS |
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.7 M (NH4)2SO4, 7% PEG 400, 100 MM HEPES, PH 7.5; THEN SOAKED IN 2 MM OF INHIBITOR SOLUTION. |
-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 44144 / % possible obs: 97.9 % / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.89→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UAG Resolution: 1.89→46.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.665 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE FOLLOWING RESIDUES WERE NOT LOCATE IN THE EXPERIMENT - GLY A 222, ALA A 223, ASP A 224, GLU A 225, GLN A 243, GLY A 244. RESIDUES ARG A 221 AND ARG A 226 WERE MODELED AS ALANINES DUE TO ...Details: THE FOLLOWING RESIDUES WERE NOT LOCATE IN THE EXPERIMENT - GLY A 222, ALA A 223, ASP A 224, GLU A 225, GLN A 243, GLY A 244. RESIDUES ARG A 221 AND ARG A 226 WERE MODELED AS ALANINES DUE TO INSUFFICIENT ELECTRON DENSITY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→46.18 Å
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Refine LS restraints |
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