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Yorodumi- PDB-3leo: Structure of human Leukotriene C4 synthase mutant R31Q in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3leo | ||||||
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Title | Structure of human Leukotriene C4 synthase mutant R31Q in complex with glutathione | ||||||
Components | Leukotriene C4 synthase | ||||||
Keywords | LYASE / Leukotriene C4 synthase / Endoplasmic reticulum / Leukotriene biosynthesis / Membrane / Nucleus / Transmembrane | ||||||
Function / homology | Function and homology information Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene biosynthetic process ...Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene biosynthetic process / glutathione peroxidase activity / nuclear outer membrane / long-chain fatty acid biosynthetic process / glutathione transferase activity / enzyme activator activity / nuclear envelope / nuclear membrane / intracellular membrane-bounded organelle / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Niegowski, D. / Martinez-Molina, D. / Rinaldo-Matthis, A. / Nordlund, P. / Haeggstrom, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Arginine 104 is a key catalytic residue in leukotriene C4 synthase. Authors: Rinaldo-Matthis, A. / Wetterholm, A. / Martinez Molina, D. / Holm, J. / Niegowski, D. / Ohlson, E. / Nordlund, P. / Morgenstern, R. / Haeggstrom, J.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3leo.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3leo.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 3leo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/3leo ftp://data.pdbj.org/pub/pdb/validation_reports/le/3leo | HTTPS FTP |
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-Related structure data
Related structure data | 2uuhS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 17251.283 Da / Num. of mol.: 1 / Mutation: R31Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: Q16873, leukotriene-C4 synthase |
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#7: Sugar | ChemComp-LMT / |
-Non-polymers , 7 types, 90 molecules
#2: Chemical | #3: Chemical | ChemComp-PLM / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GSH / | #8: Chemical | ChemComp-GOL / | #9: 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 grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2 M AmSO4, 0.1 M Bis-Tris, pH 6.5, Vapor diffusion, Sitting drop, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2008 / Details: Horizontally bended Ge(220) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. all: 31399 / Num. obs: 31117 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 20.85 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.014 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.53 / % possible all: 91.6 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UUH Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 5.699 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.111 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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