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Yorodumi- PDB-5e9h: Structural insights of isocitrate lyases from Fusarium graminearum -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e9h | ||||||
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Title | Structural insights of isocitrate lyases from Fusarium graminearum | ||||||
Components | Isocitrate lyase | ||||||
Keywords | LYASE / TIM BETA/ALPHA-BARREL / LYASE ACTIVITY | ||||||
Function / homology | Function and homology information methylisocitrate lyase / glyoxysome / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding Similarity search - Function | ||||||
Biological species | Gibberella zeae PH-1 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Park, Y. / Cho, Y. / Lee, Y.-H. / Lee, Y.-W. / Rhee, S. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e9h.cif.gz | 223.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e9h.ent.gz | 177.4 KB | Display | PDB format |
PDBx/mmJSON format | 5e9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e9h_validation.pdf.gz | 460.5 KB | Display | wwPDB validaton report |
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Full document | 5e9h_full_validation.pdf.gz | 471.9 KB | Display | |
Data in XML | 5e9h_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 5e9h_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/5e9h ftp://data.pdbj.org/pub/pdb/validation_reports/e9/5e9h | HTTPS FTP |
-Related structure data
Related structure data | 5e9fC 5e9gC 1dquS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 61971.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gibberella zeae PH-1 (fungus) / Strain: PH-1 / Gene: ICL1, FGSG_09896 / Production host: Escherichia coli (E. coli) References: UniProt: Q4HYR2, isocitrate lyase, methylisocitrate lyase #2: Chemical | ChemComp-MN / | #3: Chemical | ChemComp-MLI / | #4: Water | ChemComp-HOH / | |
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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: 2.94 Å3/Da / Density % sol: 58.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.4M SODIUM MALONATE, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
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: 2.3→50 Å / Num. obs: 64136 / % possible obs: 99.95 % / Redundancy: 21.2 % / Net I/σ(I): 19.87 |
Reflection shell | Resolution: 2.3→2.38 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DQU Resolution: 2.3→32.4 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→32.4 Å
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Refine LS restraints |
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LS refinement shell |
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