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- PDB-5hv9: Human LTC4S mutant-S36E -

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Basic information

Entry
Database: PDB / ID: 5hv9
TitleHuman LTC4S mutant-S36E
ComponentsLeukotriene C4 synthase
KeywordsLYASE / 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
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 / Leukotriene C4 synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsThulasingam, M. / Ahmad, H.R.S. / Rinaldo-Matthis, A. / Haeggstrom, J.Z.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: 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
DepositionJan 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,8573
Polymers17,4541
Non-polymers4032
Water0
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)53,5719
Polymers52,3613
Non-polymers1,2106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area8280 Å2
ΔGint-119 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.042, 168.042, 168.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-202-

SO4

21A-202-

SO4

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Components

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


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
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 5.66 Å3/Da / Density % sol: 78.28 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3→3.108 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 0.99 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.31192 400 5 %RANDOM
Rwork0.28916 ---
obs0.29032 7599 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.355 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 25 0 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9981526
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0462036
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76215152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.219158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021830
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7128.133571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.90712.194712
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.758.391547
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.93870.811799
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.993 29 -
Rwork0.937 551 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 28.6955 Å / Origin y: -14.5663 Å / Origin z: -18.4985 Å
111213212223313233
T0.297 Å20.0322 Å20.1517 Å2-0.3104 Å2-0.2662 Å2--0.4229 Å2
L2.6733 °2-0.8839 °2-1.6754 °2-0.8425 °20.843 °2--3.2043 °2
S0.1925 Å °-0.635 Å °0.7717 Å °-0.0316 Å °0.3535 Å °-0.4607 Å °-0.2721 Å °0.5455 Å °-0.546 Å °

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