+Open data
-Basic information
Entry | Database: PDB / ID: 4ntf | ||||||
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Title | Mus Musculus LTC4 synthase in S-hexyl-GSH complex form | ||||||
Components | Leukotriene C4 synthase | ||||||
Keywords | LYASE / product analogs / lipid biosynthesis | ||||||
Function / homology | Function and homology information Synthesis of 5-eicosatetraenoic acids / Synthesis of Leukotrienes (LT) and Eoxins (EX) / Synthesis of Lipoxins (LX) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / glutathione binding ...Synthesis of 5-eicosatetraenoic acids / Synthesis of Leukotrienes (LT) and Eoxins (EX) / Synthesis of Lipoxins (LX) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / glutathione binding / 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 / lipid binding / protein-containing complex binding / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å | ||||||
Authors | Niegowski, D. / Rinaldo-Matthis, A. / Haeggstrom, J.Z. | ||||||
Citation | Journal: To be Published Title: To be published Authors: Niegowski, D. / Rinaldo-Matthis, A. / Kleinschmidt, T. / Qureshi, A.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 | 4ntf.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ntf.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ntf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/4ntf ftp://data.pdbj.org/pub/pdb/validation_reports/nt/4ntf | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17657.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ltc4s / Production host: Komagataella pastoris (fungus) / References: UniProt: Q60860, leukotriene-C4 synthase |
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-Non-polymers , 5 types, 9 molecules
#2: Chemical | ChemComp-GTX / | ||||||
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#3: Chemical | ChemComp-PLM / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-NI / | #6: 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: 5.71 Å3/Da / Density % sol: 78.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.2 Details: 2.0 M NH4SO4, 0.2 M NaCl, 0.1 M Na-cacadylate, pH 6.2, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93928 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.93928 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.994→97.959 Å / Num. all: 11772 / Num. obs: 11772 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 81.54 Å2 / Rsym value: 0.06 / Net I/σ(I): 24.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.016 / Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UUI with waters, ions and lipids removed. Resolution: 2.65→48.817 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8126 / SU ML: 0.39 / σ(F): 1.36 / Phase error: 25.75 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 207.88 Å2 / Biso mean: 82.9324 Å2 / Biso min: 33.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→48.817 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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