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Yorodumi- PDB-1xg3: Crystal structure of the C123S 2-methylisocitrate lyase mutant fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xg3 | |||||||||
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Title | Crystal structure of the C123S 2-methylisocitrate lyase mutant from Escherichia coli in complex with the reaction product, Mg(II)-pyruvate and succinate | |||||||||
Components | Probable methylisocitrate lyase | |||||||||
Keywords | LYASE / 2-methylisocitrate lyase-product complex / succinate / pyruvate / isocitrate lyase superfamily | |||||||||
Function / homology | Function and homology information methylisocitrate lyase / propionate catabolic process, 2-methylcitrate cycle / methylisocitrate lyase activity / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | |||||||||
Authors | Liu, S. / Lu, Z. / Han, Y. / Melamud, E. / Dunaway-Mariano, D. / Herzberg, O. | |||||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Crystal Structures of 2-Methylisocitrate Lyase in Complex with Product and with Isocitrate Inhibitor Provide Insight into Lyase Substrate Specificity, Catalysis and Evolution Authors: Liu, S. / Lu, Z. / Han, Y. / Melamud, E. / Dunaway-Mariano, D. / Herzberg, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xg3.cif.gz | 248 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xg3.ent.gz | 197.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xg3_validation.pdf.gz | 478.5 KB | Display | wwPDB validaton report |
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Full document | 1xg3_full_validation.pdf.gz | 496.2 KB | Display | |
Data in XML | 1xg3_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 1xg3_validation.cif.gz | 79.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/1xg3 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/1xg3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Four molecules in asymmetric unit form a tetramer, which is biological unit of enzyme |
-Components
#1: Protein | Mass: 32022.355 Da / Num. of mol.: 4 / Mutation: C123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prpB / Plasmid: PET3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P77541, methylisocitrate lyase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PYR / #4: Chemical | #5: 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: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% PEG3350, 0.1M (NH)2SO4, 0.1M MES (pH6.0). 5mM Mg(II), 5mM isocitrate, followed by overnight soaking of a crystal in 35% PEG3350, 100 mM succinate, 100 mM pyruvate, 5mM Mg(II), VAPOR ...Details: 30% PEG3350, 0.1M (NH)2SO4, 0.1M MES (pH6.0). 5mM Mg(II), 5mM isocitrate, followed by overnight soaking of a crystal in 35% PEG3350, 100 mM succinate, 100 mM pyruvate, 5mM Mg(II), VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 18, 2004 / Details: focusing mirrors (MSC/Yale) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25.85 Å / Num. all: 100609 / Num. obs: 89039 / % possible obs: 88.5 % / Observed criterion σ(I): 1 / Redundancy: 2.82 % / Rmerge(I) obs: 0.025 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.084 / % possible all: 67.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: structure of the C123S mutant enzyme in complex with isocitrate Resolution: 1.9→25.85 Å / Cross valid method: throught / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→25.85 Å
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Refine LS restraints |
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Xplor file |
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