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Yorodumi- PDB-2rl1: Crystal structure of UDP-N-acetylglucosamine enolpyruvyl transfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rl1 | ||||||
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Title | Crystal structure of UDP-N-acetylglucosamine enolpyruvyl transferase from Haemophilus influenzae in complex with UDP-N-acetylglucosamine | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
Keywords | TRANSFERASE / MurA / MurZ / UDP-N-acetylglucosamine / Cell cycle / Cell division / Cell shape / Cell wall biogenesis/degradation / Cytoplasm / Peptidoglycan synthesis | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Yoon, H.J. / Suh, S.W. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of UDP-N-acetylglucosamine enolpyruvyl transferase from Haemophilus influenzae in complex with UDP-N-acetylglucosamine and fosfomycin Authors: Yoon, H.J. / Lee, S.J. / Mikami, B. / Park, H.J. / Yoo, J. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rl1.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rl1.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 2rl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/2rl1 ftp://data.pdbj.org/pub/pdb/validation_reports/rl/2rl1 | HTTPS FTP |
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-Related 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: 45236.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: MurZ / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: P45025, UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-UD1 / |
#4: 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: 2.78 Å3/Da / Density % sol: 55.71 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 1.8M ammonium sulfate, 5-10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. obs: 52873 / % possible obs: 99.7 % / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.73→1.79 Å / Rmerge(I) obs: 0.35 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Resolution: 2.2→30 Å / σ(F): 320
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Solvent computation | Bsol: 55.707 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.634 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Xplor file |
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