+Open data
-Basic information
Entry | Database: PDB / ID: 5hv9 | ||||||
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Title | Human LTC4S mutant-S36E | ||||||
Components | Leukotriene C4 synthase | ||||||
Keywords | LYASE / LTC4S / mutant | ||||||
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 / Resolution: 3 Å | ||||||
Authors | Thulasingam, M. / Ahmad, H.R.S. / Rinaldo-Matthis, A. / Haeggstrom, J.Z. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Phosphorylation of Leukotriene C4 Synthase at Serine 36 Impairs Catalytic Activity. Authors: Ahmad, S. / Ytterberg, A.J. / Thulasingam, M. / Tholander, F. / Bergman, T. / Zubarev, R. / Wetterholm, A. / Rinaldo-Matthis, A. / 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 | 5hv9.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hv9.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/5hv9 ftp://data.pdbj.org/pub/pdb/validation_reports/hv/5hv9 | HTTPS FTP |
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-Related structure data
Related structure data | 2uuiS 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: 17453.580 Da / Num. of mol.: 1 / Mutation: S36E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LTC4S / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: Q16873, leukotriene-C4 synthase |
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#2: Chemical | ChemComp-GSH / |
#3: Chemical | ChemComp-SO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.66 Å3/Da / Density % sol: 78.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.0 M NH4SO4, 0.2 M NaCl, 0.1 M Na-cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3→42.01 Å / Num. obs: 7999 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 13.4 % / Biso Wilson estimate: 139.42 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09035 / Net I/σ(I): 20.57 |
Reflection shell | Resolution: 3→3.108 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 0.99 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UUI Resolution: 3→42.01 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.806 / SU B: 46.31 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.361 / 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: 114.355 Å2
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Refinement step | Cycle: LAST / Resolution: 3→42.01 Å
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Refine LS restraints |
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