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- PDB-4j7y: Human LTC4 synthase in complex with product analogs - implication... -

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Basic information

Entry
Database: PDB / ID: 4j7y
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 / 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
Chem-1JP / NICKEL (II) ION / Leukotriene C4 synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.901 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 / pdbx_struct_special_symmetry / 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)18,0204
Polymers17,4121
Non-polymers6083
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)54,05912
Polymers52,2353
Non-polymers1,8259
Water0
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 area7560 Å2
ΔGint-113 kcal/mol
Surface area20570 Å2
MethodPISA
2
A: Leukotriene C4 synthase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)216,23848
Polymers208,93912
Non-polymers7,29936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation21_554y,z+1/2,x-1/21
crystal symmetry operation22_554-y,z+1/2,-x-1/21
crystal symmetry operation23_544y,-z-1/2,-x-1/21
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation29_554z+1/2,x,y-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
crystal symmetry operation31_454-z-1/2,-x,y-1/21
crystal symmetry operation32_454-z-1/2,x,-y-1/21
Buried area35840 Å2
ΔGint-497 kcal/mol
Surface area77530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.275, 169.275, 169.275
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-201-

NI

21A-202-

SO4

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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 / 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-1JP / D-gamma-glutamyl-(Z)-N-(carboxymethylidene)-S-[(2R)-2-hydroxy-4-phenylbutyl]-L-cysteinamide


Mass: 453.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O7S

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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: 5.8 Å3/Da / Density % sol: 78.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.2
Details: 1.8 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: 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: 2.901→32.653 Å / Num. all: 9030 / Num. obs: 9030 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.6 % / Rsym value: 0.292 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.9-3.0615.70.0610.16.1341100
3.06-3.2415.90.0610.23.4771100
3.24-3.4715.80.0610.41.9611100
3.47-3.7415.80.0610.90.8811100
3.74-4.115.80.0611.90.3981100
4.1-4.5915.70.06140.1761100
4.59-5.2915.50.0614.40.1581100
5.29-6.4815.50.0613.80.1891100
6.48-9.1714.80.0614.30.121100
9.17-34.553140.06150.108197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.42 Å29.92 Å
Translation6.42 Å29.92 Å

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Processing

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

2uui


Resolution: 2.901→29.924 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.59 / σ(F): 1.33 / Phase error: 33.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 439 4.87 %
Rwork0.2495 --
obs0.2502 9020 99.88 %
all-9020 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.4109 Å2
Refinement stepCycle: LAST / Resolution: 2.901→29.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 37 0 1193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061226
X-RAY DIFFRACTIONf_angle_d1.41670
X-RAY DIFFRACTIONf_dihedral_angle_d15.643426
X-RAY DIFFRACTIONf_chiral_restr0.115190
X-RAY DIFFRACTIONf_plane_restr0.006208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9013-3.32070.38681550.34842830X-RAY DIFFRACTION100
3.3207-4.18190.27871280.27892846X-RAY DIFFRACTION100
4.1819-29.92550.2331560.22152905X-RAY DIFFRACTION100

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