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- PDB-3su9: E. Cloacae MURA in complex with UDP-N-acetylmuramic acid and cova... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3su9 | ||||||
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Title | E. Cloacae MURA in complex with UDP-N-acetylmuramic acid and covalent adduct of PEP with Cys115 | ||||||
![]() | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
![]() | TRANSFERASE / MURA / CLOSE ENZYME STATE / BIOGENESIS/DEGRADATION / PEPTIDOGLYCAN SYNTHESIS / Covalent adduct of PEP | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhu, J.-Y. / Yang, Y. / Schonbrunn, E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.6 KB | Display | ![]() |
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PDB format | ![]() | 77.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3spbC ![]() 3swaC ![]() 3swdC ![]() 3sweC ![]() 3swgC ![]() 3swiC ![]() 3swqC ![]() 3upkC ![]() 3v4tC ![]() 3v5vC ![]() 3kqaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 44997.449 Da / Num. of mol.: 1 / Mutation: N67D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-EPZ / ( | #5: Water | ChemComp-HOH / | Sequence details | IAS67 FORMS AN ISOPEPTIDI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 mg/mL MurA, 25 mM HEPES, 100 mM Ammonium Acetate, 50 mM Bis-Tris, 12.5 % PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 14, 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: 2.2→20 Å / Num. obs: 22499 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 5.7 / Net I/σ(I): 33.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 5.7 / Rsym value: 36.3 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3KQA Resolution: 2.2→19.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6882367.51 / 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: 40.8015 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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