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Yorodumi- PDB-4jrz: Human LTC4 synthase in complex with product analogs - implication... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jrz | ||||||
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Title | Human LTC4 synthase in complex with product analogs - implications for enzyme catalysis | ||||||
Components | Leukotriene C4 synthase | ||||||
Keywords | LYASE / Leukotriene C4 synthase / product analogs / lipid biosynthesis | ||||||
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 / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Niegowski, D. / Rinaldo-Matthis, A. / Haeggstrom, J.Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal Structures of Leukotriene C4 Synthase in Complex with Product Analogs: IMPLICATIONS FOR THE ENZYME MECHANISM. Authors: Niegowski, D. / Kleinschmidt, T. / Olsson, U. / Ahmad, S. / 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 | 4jrz.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jrz.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jrz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jrz_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4jrz_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4jrz_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 4jrz_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/4jrz ftp://data.pdbj.org/pub/pdb/validation_reports/jr/4jrz | HTTPS FTP |
-Related structure data
Related structure data | 4j7tC 4j7yC 4jc7C 4jczC 2uuiS S: Starting model for refinement C: citing same article (ref.) |
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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: 17372.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LTC4S / Production host: Pichia Pastoris (fungus) / References: UniProt: Q16873, leukotriene-C4 synthase |
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-Non-polymers , 6 types, 33 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-PAM / | #5: Chemical | ChemComp-PLM / #6: Chemical | ChemComp-GTX / | #7: 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 / pH: 6.4 Details: 2.2 M NH4SO4, 0.2 M NaCl, 0.1 M Na-cacadylate, pH 6.4, VAPOR DIFFUSION, temperature 298K |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.93927 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→20.728 Å / Num. all: 15351 / Num. obs: 15351 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.072 / Net I/σ(I): 9.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UUI Resolution: 2.4→20.66 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7782 / SU ML: 0.3 / σ(F): 1.35 / Phase error: 29.17 / 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: 114.47 Å2 / Biso mean: 59.5193 Å2 / Biso min: 28.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20.66 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: 5
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