+Open data
-Basic information
Entry | Database: PDB / ID: 4nta | ||||||
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Title | Mus Musculus LTC4 synthase in apo 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: 2.7 Å | ||||||
Authors | Niegowski, D. / Rinaldo-Matthis, A. / Haeggstrom, J.Z. | ||||||
Citation | Journal: To be Published Title: Mus Musculus LTC4 synthase in apo form 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 | 4nta.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nta.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/4nta ftp://data.pdbj.org/pub/pdb/validation_reports/nt/4nta | 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
#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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#2: Chemical | ChemComp-PLM / #3: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.75 Å3/Da / Density % sol: 78.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.3 Details: 1.9 M NH4SO4, 0.2 M NaCl, 0.1 M Na-cacadylate, pH 6.3, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.999→97.959 Å / Num. all: 11165 / Num. obs: 11165 / % possible obs: 99.5 % / Observed criterion σ(F): 2.092 / Redundancy: 3.3 % / Biso Wilson estimate: 85.54 Å2 / Rsym value: 0.046 / Net I/σ(I): 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | 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: PDB entry 2UUI Resolution: 2.7→42.394 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7752 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 29.18 / 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: 264.04 Å2 / Biso mean: 83.5864 Å2 / Biso min: 28.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→42.394 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
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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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