+Open data
-Basic information
Entry | Database: PDB / ID: 4e7e | ||||||
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Title | E. cloacae C115D MurA in complex with UDP-glucose | ||||||
Components | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
Keywords | TRANSFERASE / open enzyme state / cell wall / biogenesis/degradation / 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 | Enterobacter cloacae subsp. cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhu, J.-Y. / Yang, Y. / Schonbrunn, E. | ||||||
Citation | Journal: To be Published Title: Open-close transition of MurA Authors: Zhu, J.-Y. / Yang, Y. / Betzi, 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 | 4e7e.cif.gz | 333.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e7e.ent.gz | 269.5 KB | Display | PDB format |
PDBx/mmJSON format | 4e7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/4e7e ftp://data.pdbj.org/pub/pdb/validation_reports/e7/4e7e | HTTPS FTP |
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-Related structure data
Related structure data | 4e7bC 4e7cC 4e7dC 4e7fC 4e7gC 4eiiC 3spbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44841.352 Da / Num. of mol.: 4 / Mutation: C115D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (bacteria) Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_04571, murA, murZ / Plasmid: pET9D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.44 Å3/Da / Density % sol: 49.69 % |
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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-glucose, 25 mM HEPES, pH 7.5, 0.1 M ammonium sulfate, 50 mM Bis-Tris, pH 5.5, 12.5% PEG3350, 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: Apr 10, 2010 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 78625 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.053 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.29 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SPB Resolution: 2.3→19.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3881792.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.1604 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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