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Open data
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Basic information
Entry | Database: PDB / ID: 4e7c | ||||||
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Title | E. cloacae MurA in complex with UTP | ||||||
![]() | UDP-N-acetylglucosamine 1-carboxyvinyltransferase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 342.7 KB | Display | ![]() |
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PDB format | ![]() | 276.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4e7bC ![]() 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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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, ![]() #2: Chemical | ChemComp-EDO / ![]() #3: Chemical | ChemComp-ACT / ![]() #4: Chemical | ![]() #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: 2.44 Å3/Da / Density % sol: 49.63 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 mg/mL MurA, 5 mM UTP, 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: May 28, 2010 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→20 Å / Num. obs: 100459 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.068 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.341 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3SPB Resolution: 2.1→19.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3613873.17 / 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: 52.8868 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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