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- PDB-4j7t: Human LTC4 synthase in complex with product analogs - implication... -

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Basic information

Entry
Database: PDB / ID: 4j7t
TitleHuman LTC4 synthase in complex with product analogs - implications for enzyme catalysis
ComponentsLeukotriene C4 synthase
KeywordsLYASE / 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 / Biosynthesis 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) / glutathione peroxidase activity ...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 / Biosynthesis 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) / glutathione peroxidase activity / leukotriene biosynthetic process / 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
Chem-1JO / NICKEL (II) ION / Leukotriene C4 synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.203 Å
AuthorsNiegowski, D. / Rinaldo-Matthis, A. / Haeggstrom, J.Z.
CitationJournal: 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
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Mar 12, 2014Group: Database references
Revision 1.3Sep 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)18,0064
Polymers17,4121
Non-polymers5943
Water00
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)54,01712
Polymers52,2353
Non-polymers1,7839
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area7370 Å2
ΔGint-82 kcal/mol
Surface area20510 Å2
MethodPISA
2
A: Leukotriene C4 synthase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)216,07048
Polymers208,93912
Non-polymers7,13136
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area36720 Å2
ΔGint-494 kcal/mol
Surface area76580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.392, 168.392, 168.392
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-201-

NI

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Components

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


Mass: 17411.545 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
#2: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1JO / D-gamma-glutamyl-S-(4-phenylbutyl)-L-cysteinylglycine


Mass: 439.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N3O6S

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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: 78.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.4
Details: 1.9 M NH4SO4, 0.2 M NaCl, 0.1 M Na-cacodylate, pH 6.4, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93937 Å / Relative weight: 1
ReflectionResolution: 3.203→37.939 Å / Num. all: 6634 / Num. obs: 6634 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.6 % / Rsym value: 0.182 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.2-3.3713.80.711131499520.71100
3.37-3.5813.90.4571.5127579190.457100
3.58-3.8213.80.2922.3117728550.292100
3.82-4.1313.80.2162.9108847900.216100
4.13-4.5313.70.1843.299767290.184100
4.53-5.0613.60.1723.591276710.172100
5.06-5.8413.60.1882.980825960.188100
5.84-7.1613.20.1663.367165080.166100
7.16-10.1212.90.1313.350703940.131100
10.12-37.65412.10.1153.526652200.11593.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.38 Å37.65 Å
Translation6.38 Å37.65 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UUI

2uui


Resolution: 3.203→37.654 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8353 / SU ML: 0.38 / σ(F): 1.38 / σ(I): 2 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 320 4.83 %Rfree-column copied from 2UUI
Rwork0.2198 ---
obs0.221 6625 99.79 %-
all-6634 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.71 Å2 / Biso mean: 64.873 Å2 / Biso min: 18.63 Å2
Refinement stepCycle: LAST / Resolution: 3.203→37.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 0 36 0 1195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051229
X-RAY DIFFRACTIONf_angle_d1.3121673
X-RAY DIFFRACTIONf_chiral_restr0.114189
X-RAY DIFFRACTIONf_plane_restr0.006208
X-RAY DIFFRACTIONf_dihedral_angle_d15.784433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.203-4.03470.26281530.223931223275
4.0347-37.65620.23931670.218131833350

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