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Yorodumi- PDB-3b29: Human leukotriene C4 synthase in complex with dodecyl-beta-D-sele... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b29 | ||||||
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Title | Human leukotriene C4 synthase in complex with dodecyl-beta-D-selenomaltoside | ||||||
Components | Leukotriene C4 synthase | ||||||
Keywords | LYASE / membrane protein / helix bundle / homo trimer / mGST / MAPEG | ||||||
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 / MAD / Resolution: 3.2 Å | ||||||
Authors | Saino, H. / Ago, H. / Miyano, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Seleno-detergent MAD phasing of leukotriene C4 synthase in complex with dodecyl-beta-D-selenomaltoside Authors: Saino, H. / Ago, H. / Ukita, Y. / Miyano, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b29.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b29.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 3b29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/3b29 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/3b29 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 17411.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LTC4S / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q16873, leukotriene-C4 synthase | ||
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#2: Chemical | ChemComp-GSH / | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Sugar | ChemComp-LSM / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.73 Å3/Da / Density % sol: 78.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES-NaOH, 1.6M ammonium sulfate, 0.4M magnesium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97909, 0.97938, 0.97600, 0.98300 | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2011 | |||||||||||||||
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→26.6 Å / Num. obs: 6018 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Rmerge(I) obs: 0.125 | |||||||||||||||
Reflection shell | Highest resolution: 3.2 Å / Redundancy: 22 % / Rmerge(I) obs: 0.13 / Num. unique all: 6018 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.2→25.42 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.874 / SU B: 10.637 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.642 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→25.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.202→3.573 Å / Total num. of bins used: 5
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