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Yorodumi- PDB-3swi: E. Cloacae MurA in complex with Enolpyruvyl-UDP-N-acetylgalactosa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3swi | ||||||
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Title | E. Cloacae MurA in complex with Enolpyruvyl-UDP-N-acetylgalactosamine and covalent adduct of PEP with CYS115 | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
Keywords | TRANSFERASE / MURA / CLOSE ENZYME STATE / CELL WALL / BIOGENESIS/DEGRADATION / PEPTIDOGLYCAN SYNTHESIS / PEP | ||||||
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 division / cytoplasm Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Zhu, J.-Y. / Yang, Y. / Schonbrunn, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Functional Consequence of Covalent Reaction of Phosphoenolpyruvate with UDP-N-acetylglucosamine 1-Carboxyvinyltransferase (MurA). Authors: Zhu, J.Y. / Yang, Y. / Han, H. / Betzi, S. / Olesen, S.H. / Marsilio, F. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3swi.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3swi.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 3swi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/3swi ftp://data.pdbj.org/pub/pdb/validation_reports/sw/3swi | HTTPS FTP |
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-Related structure data
Related structure data | 3spbC 3su9SC 3swaC 3swdC 3sweC 3swgC 3swqC 3upkC 3v4tC 3v5vC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44997.449 Da / Num. of mol.: 1 / Mutation: N67D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: murA, murZ, ECL_04571 / Plasmid: PET9D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase |
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-Non-polymers , 6 types, 121 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-UD2 / | #6: Chemical | ChemComp-UPN / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | IAS67 FORMS AN ISOPEPTIDI |
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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: 2.4 Å3/Da / Density % sol: 48.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 mg/mL MurA, 5 mM UDP-N-ACETYLGALACTOSAMINE, 2.5 mM PEP, 75 mM HEPES, 25 mM Magnesium Chloride, 15% PEG 550 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 23, 2010 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 10689 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 6.6 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8 / Rsym value: 26.7 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3SU9 Resolution: 2.8→19.43 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 7475233.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.5316 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
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