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- PDB-3hkk: Structure of human Leukotriene C4 synthase in complex with glutat... -

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Basic information

Entry
Database: PDB / ID: 3hkk
TitleStructure of human Leukotriene C4 synthase in complex with glutathione sulfonate
ComponentsLeukotriene C4 synthase
KeywordsLYASE / Leukotriene C4 synthase / Leukotriene biosynthesis / Membrane / Nucleus / Polymorphism / Transmembrane
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
5-lipoxygenase-activating protein / FLAP/GST2/LTC4S, conserved site / FLAP/GST2/LTC4S family signature. / Membrane associated eicosanoid/glutathione metabolism-like domain / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTATHIONE SULFONIC ACID / PALMITOLEIC ACID / PALMITIC ACID / Leukotriene C4 synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRinaldo-Matthis, A. / Haeggstrom, J.Z.
CitationJournal: To be Published
Title: Pre-steady state kinetics of human Leukotriene C4 synthase
Authors: Rinaldo-Matthis, A. / Wetterholm, A. / Holm, J. / Ohlsson, E. / Tibbelin, G. / Morgenstern, R. / Haeggstrom, J.Z.
History
DepositionMay 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5609
Polymers17,4121
Non-polymers2,1488
Water1,11762
1
A: Leukotriene C4 synthase
hetero molecules

A: Leukotriene C4 synthase
hetero molecules

A: Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,67927
Polymers52,2353
Non-polymers6,44524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_555z,-x+1/2,-y+1/21
crystal symmetry operation48_555-y+1/2,-z+1/2,x1
Buried area15790 Å2
ΔGint-20 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.718, 170.718, 170.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

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Components

#1: Protein Leukotriene C4 synthase / Leukotriene-C(4) synthase / LTC4 synthase


Mass: 17411.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPICZ / Production host: Pichia Pastoris (fungus) / Strain (production host): KM71H / References: UniProt: Q16873, leukotriene-C4 synthase
#2: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O9S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.9532 Å3/Da / Density % sol: 79.339 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2M AmSO4, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 30, 2009
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→98.564 Å / Num. obs: 9259 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.1 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.145 / Rsym value: 0.145 / Net I/σ(I): 4.856
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 25.4 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 0.9 / Num. measured all: 33674 / Num. unique all: 1328 / Rsym value: 0.855 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
PXSOFTdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2uuh

2uuh


Resolution: 2.9→38.18 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.175 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.873 / SU B: 8.189 / SU ML: 0.162 / SU R Cruickshank DPI: 0.333 / SU Rfree: 0.265 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.333 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 440 4.8 %RANDOM
Rwork0.185 ---
all0.187 ---
obs0.187 9214 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.36 Å2 / Biso mean: 46.433 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 87 62 1284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221244
X-RAY DIFFRACTIONr_angle_refined_deg1.5822.0241668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70519.78747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22715174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9191513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02897
X-RAY DIFFRACTIONr_nbd_refined0.2370.2558
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2837
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.210
X-RAY DIFFRACTIONr_mcbond_it0.7611.5739
X-RAY DIFFRACTIONr_mcangle_it1.39821144
X-RAY DIFFRACTIONr_scbond_it1.8043567
X-RAY DIFFRACTIONr_scangle_it2.9544.5524
LS refinement shellResolution: 2.904→2.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 31 -
Rwork0.221 611 -
all-642 -
obs--100 %

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