+Open data
-Basic information
Entry | Database: PDB / ID: 2jfg | ||||||
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Title | Crystal structure of MurD ligase in complex with UMA and ADP | ||||||
Components | UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE | ||||||
Keywords | LIGASE / NUCLEOTIDE-BINDING / PEPTIDOGLYCAN SYNTHESIS / MURD LIGASE / ATP-BINDING / CELL DIVISION / UMA / ADP / CELL WALL / CELL SHAPE / CELL CYCLE | ||||||
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: 1.52 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 | 2jfg.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jfg.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 2jfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/2jfg ftp://data.pdbj.org/pub/pdb/validation_reports/jf/2jfg | HTTPS FTP |
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-Related structure data
Related structure data | 2jffC 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: UMA AND ADP 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-UMA / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-SO4 / |
#5: 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 Å3/Da / Density % sol: 59 % 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 |
-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 2, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→65 Å / Num. obs: 82385 / % possible obs: 96.3 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 31 |
Reflection shell | Resolution: 1.52→1.61 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.7 / % possible all: 91.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UAG Resolution: 1.52→65.09 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 14.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→65.09 Å
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Refine LS restraints |
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