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- PDB-4ntb: Mus Musculus LTC4 synthase in GSH complex form -

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Basic information

Entry
Database: PDB / ID: 4ntb
TitleMus Musculus LTC4 synthase in GSH complex form
ComponentsLeukotriene C4 synthase
KeywordsLYASE / 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
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 / NICKEL (II) ION / PALMITIC ACID / Leukotriene C4 synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsNiegowski, D. / Rinaldo-Matthis, A. / Haeggstrom, J.Z.
CitationJournal: To be Published
Title: Mus Musculus LTC4 synthase in GSH complex form
Authors: Niegowski, D. / Rinaldo-Matthis, A. / Kleinschmidt, T. / Qureshi, A.A. / Haeggstrom, J.Z.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Leukotriene C4 synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8897
Polymers17,6581
Non-polymers1,2316
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)56,66821
Polymers52,9743
Non-polymers3,69418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area12330 Å2
ΔGint-92 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.297, 169.297, 169.297
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

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Components

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


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
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2

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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: 5.72 Å3/Da / Density % sol: 78.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.2
Details: 2.1 M NH4SO4, 0.2 M NaCl, 0.1 M Na-cacadylate, pH 6.2, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9399 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9399 Å / Relative weight: 1
ReflectionResolution: 1.996→97.959 Å / Num. all: 11166 / Num. obs: 11166 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 73.41 Å2 / Rsym value: 0.079 / Net I/σ(I): 21.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.7-2.8510.40.0130.61.2951100
2.85-3.0211.50.0130.80.921100
3.02-3.2311.30.0131.30.5691100
3.23-3.4911.30.0132.70.2811100
3.49-3.8211.20.0135.50.1351100
3.82-4.2711.30.01310.80.0681100
4.27-4.9311.30.01316.20.0441100
4.93-6.0411.30.01315.40.0461100
6.04-8.5410.90.01319.50.0341100
8.54-28.21610.50.01326.90.02197.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.94 Å28.22 Å
Translation3.94 Å28.22 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2UUI with water

2uui


Resolution: 2.7→28.216 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 548 4.91 %
Rwork0.2121 --
obs0.2135 11164 99.98 %
all-11165 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.7568 Å2
Refinement stepCycle: LAST / Resolution: 2.7→28.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 54 0 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011256
X-RAY DIFFRACTIONf_angle_d1.2781700
X-RAY DIFFRACTIONf_dihedral_angle_d16.866442
X-RAY DIFFRACTIONf_chiral_restr0.082189
X-RAY DIFFRACTIONf_plane_restr0.006208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.97170.26761450.24422618X-RAY DIFFRACTION100
2.9717-3.40110.29711360.22462638X-RAY DIFFRACTION100
3.4011-4.28260.22051220.19862657X-RAY DIFFRACTION100
4.2826-28.21770.23031450.21142703X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0045-0.00290.00030.00440.00110.0009-0.00570.0136-0.016-0.0273-0.0163-0.0044-0.0050.00790.00030.90520.26530.24380.6848-0.15610.732127.2094-38.4409-34.5789
20.2526-0.2209-0.16420.25140.10320.15160.0336-0.21860.06390.2437-0.05330.5174-0.1249-0.40630.14060.04230.42160.60780.1183-0.39860.475210.6389-26.2869-16.4994
30.04620.08060.0670.15970.09940.08260.1695-0.23990.02630.55560.08840.10490.1231-0.14970.11530.51240.26360.11070.54930.01190.431433.3643-34.3764-10.1338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 99 )
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 145 )

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