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Open data
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Basic information
Entry | Database: PDB / ID: 5e9g | ||||||
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Title | Structural insights of isocitrate lyases from Magnaporthe oryzae | ||||||
![]() | Isocitrate lyase | ||||||
![]() | LYASE / TIM BETA/ALPHA-BARREL / LYASE ACTIVITY | ||||||
Function / homology | ![]() methylisocitrate lyase / methylisocitrate lyase activity / isocitrate lyase / glyoxysome / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, Y. / Cho, Y. / Lee, Y.-H. / Lee, Y.-W. / Rhee, S. | ||||||
![]() | ![]() Title: Crystal structure and functional analysis of isocitrate lyases from Magnaporthe oryzae and Fusarium graminearum Authors: Park, Y. / Cho, Y. / Lee, Y.-H. / Lee, Y.-W. / Rhee, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 402.1 KB | Display | ![]() |
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PDB format | ![]() | 327.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.1 KB | Display | ![]() |
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Full document | ![]() | 548.5 KB | Display | |
Data in XML | ![]() | 75 KB | Display | |
Data in CIF | ![]() | 101.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e9fC ![]() 5e9hC ![]() 1dquS 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: 62625.793 Da / Num. of mol.: 4 / Mutation: A219G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P0CT06, isocitrate lyase, methylisocitrate lyase #2: Chemical | ChemComp-GLV / #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M POTASSIUM SODIUM TARTRATE, 20% PEG-3350, 10% (V/V) GLYCEROL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 142312 / % possible obs: 93.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.404 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DQU Resolution: 2.1→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Bsol: 38.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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Xplor file |
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