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- PDB-4ntf: Mus Musculus LTC4 synthase in S-hexyl-GSH complex form -

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Basic information

Entry
Database: PDB / ID: 4ntf
TitleMus Musculus LTC4 synthase in S-hexyl-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) / Biosynthesis 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) / Biosynthesis 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 / glutathione transferase activity / enzyme activator activity / lipid metabolic process / nuclear envelope / nuclear membrane / lipid binding / endoplasmic reticulum membrane / protein-containing complex binding / endoplasmic reticulum
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
S-HEXYLGLUTATHIONE / 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: 2.65 Å
AuthorsNiegowski, D. / Rinaldo-Matthis, A. / Haeggstrom, J.Z.
CitationJournal: To be Published
Title: To be published
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)19,2318
Polymers17,6581
Non-polymers1,5737
Water362
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)57,69224
Polymers52,9743
Non-polymers4,71921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
Buried area12050 Å2
ΔGint-45 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.107, 169.107, 169.107
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-207-

NI

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 9 molecules

#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 5.71 Å3/Da / Density % sol: 78.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.2
Details: 2.0 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: ESRF / Beamline: ID29 / Wavelength: 0.93928 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93928 Å / Relative weight: 1
ReflectionResolution: 1.994→97.959 Å / Num. all: 11772 / Num. obs: 11772 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 81.54 Å2 / Rsym value: 0.06 / Net I/σ(I): 24.7
Reflection shell

Rmerge(I) obs: 0.016 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.65-2.798.40.51428716991.576100
2.79-2.9611.70.71879616121.084100
2.96-3.1711.61.21763215260.628100
3.17-3.4211.22.51569314060.297100
3.42-3.7511.75.51514612950.137100
3.75-4.191112.31296211810.06100
4.19-4.8411.720.51230310550.035100
4.84-5.9311.219.799988950.035100
5.93-8.38112177006980.029100
8.38-48.81710.513.242554050.02399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UUI with waters, ions and lipids removed.

2uui


Resolution: 2.65→48.817 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8126 / SU ML: 0.39 / σ(F): 1.36 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 584 4.96 %Copied R-Free from PDB ID 2UUI: Random
Rwork0.2159 ---
obs0.2173 11766 99.95 %-
all-11772 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.88 Å2 / Biso mean: 82.9324 Å2 / Biso min: 33.08 Å2
Refinement stepCycle: LAST / Resolution: 2.65→48.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 70 2 1228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011254
X-RAY DIFFRACTIONf_angle_d1.3671689
X-RAY DIFFRACTIONf_chiral_restr0.095186
X-RAY DIFFRACTIONf_plane_restr0.007205
X-RAY DIFFRACTIONf_dihedral_angle_d15.863445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6501-2.91670.32111530.270327842937
2.9167-3.33870.30881500.232827442894
3.3387-4.20610.2431270.205228012928
4.2061-48.82520.22411540.211528533007
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)
10.7864-0.37611.03960.2114-0.37821.66140.617-0.545-0.8320.2963-0.4119-1.36280.51110.66172.86211.47891.5791-0.32951.21690.52560.824227.1802-32.7792-45.9572
21.7381-1.0623-0.99053.12051.36791.21490.1077-0.23650.3428-0.5171-0.04110.7147-0.5195-1.3602-0.00380.60550.2387-0.12860.83260.19770.72049.686-17.3434-61.5802
32.14711.34511.00242.1192-0.62173.00730.01-0.34940.82070.7397-0.10310.1353-1.4565-0.63510.20030.72390.2366-0.19480.3967-0.06940.563725.7204-11.7023-50.387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 73 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 145 )A0

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