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Open data
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Basic information
Entry | Database: PDB / ID: 5jy4 | ||||||||||||
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Title | A high magnesium structure of the isochorismate synthase, EntC | ||||||||||||
![]() | (Isochorismate synthase EntC) x 2 | ||||||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Meneely, K.M. / Sundlov, J.A. / Gulick, A.M. / Lamb, A.L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: An Open and Shut Case: The Interaction of Magnesium with MST Enzymes. Authors: Meneely, K.M. / Sundlov, J.A. / Gulick, A.M. / Moran, G.R. / Lamb, A.L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.9 KB | Display | ![]() |
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PDB format | ![]() | 230.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5jxzC ![]() 5jy8C ![]() 5jy9C ![]() 5jzdC ![]() 3hwoS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42992.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 42976.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.28 % |
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Crystal grow![]() | Temperature: 298.15 K / Method: microbatch / pH: 6.2 Details: 0.1 M MES pH 6.2, 50% PEG 200, 0.05 M ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2016 / Details: Mirror: Rh coated |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.11→38.9 Å / Num. obs: 51991 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rsym value: 0.074 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.11→2.17 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.031 / Mean I/σ(I) obs: 2 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3HWO Resolution: 2.11→38.898 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→38.898 Å
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Refine LS restraints |
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LS refinement shell |
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