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Yorodumi- PDB-1dlg: CRYSTAL STRUCTURE OF THE C115S ENTEROBACTER CLOACAE MURA IN THE U... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dlg | ||||||
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Title | CRYSTAL STRUCTURE OF THE C115S ENTEROBACTER CLOACAE MURA IN THE UN-LIGANDED STATE | ||||||
Components | UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE MURA | ||||||
Keywords | TRANSFERASE / inside-out alpha/beta barrel | ||||||
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 | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Schonbrunn, E. / Eschenburg, S. / Krekel, F. / Luger, K. / Amrhein, N. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Role of the loop containing residue 115 in the induced-fit mechanism of the bacterial cell wall biosynthetic enzyme MurA. Authors: Schonbrunn, E. / Eschenburg, S. / Krekel, F. / Luger, K. / Amrhein, N. #1: Journal: To be Published Title: Comparative X-ray analysis of the un-liganded fosfomycin target MurA Authors: Eschenburg, S. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dlg.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dlg.ent.gz | 155.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/1dlg ftp://data.pdbj.org/pub/pdb/validation_reports/dl/1dlg | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | the asymmetric unit contains a homodimer (monomer A and monomer B) |
-Components
#1: Protein | Mass: 44813.344 Da / Num. of mol.: 2 / Mutation: C115S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.95 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.4-0.8 M sodium/potassium phosphate including 20-40 mM cyclohexylammonium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K, temperature 292K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.9 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8729 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→14.97 Å / Num. all: 703604 / Num. obs: 86085 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 35.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2 % / Rmerge(I) obs: 0.119 / Num. unique all: 3179 / % possible all: 91.9 |
Reflection | *PLUS Num. measured all: 703604 |
Reflection shell | *PLUS % possible obs: 91.9 % / Mean I/σ(I) obs: 5.9 |
-Processing
Software |
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Refinement | Resolution: 1.9→14.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 2498822.11 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: used 4 round of simulated annealing/minimization/bindividual refinement by CNS
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Displacement parameters | Biso mean: 24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.173 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.246 / % reflection Rfree: 3.1 % / Rfactor Rwork: 0.205 |