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Open data
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Basic information
Entry | Database: PDB / ID: 4e7b | ||||||
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Title | E. cloacae MurA in complex with UDP-glucose | ||||||
![]() | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | ||||||
![]() | TRANSFERASE / open enzyme state / cell wall / biogenesis/degradation / peptidoglycan synthesis | ||||||
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 cycle / cell division / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhu, J.-Y. / Yang, Y. / Schonbrunn, E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 353.2 KB | Display | ![]() |
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PDB format | ![]() | 284.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 78.2 KB | Display | |
Data in CIF | ![]() | 110.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4e7cC ![]() 4e7dC ![]() 4e7eC ![]() 4e7fC ![]() 4e7gC ![]() 4eiiC ![]() 3spbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44829.406 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_04571, murA, murZ / Plasmid: pET9D / Production host: ![]() ![]() References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-UPG / #5: Water | ChemComp-HOH / | Sequence details | IAS67 FORMS AN ISOPEPTIDI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.02 % |
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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: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 15, 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→20 Å / Num. obs: 118332 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.039 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.189 / % possible all: 92.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3SPB Resolution: 2→19.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3629139.5 / 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: 52.3729 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.96 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→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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