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- PDB-2uui: Crystal structure of Human Leukotriene C4 Synthase -

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Basic information

Entry
Database: PDB / ID: 2uui
TitleCrystal structure of Human Leukotriene C4 Synthase
ComponentsLEUKOTRIENE C4 SYNTHASE
KeywordsLYASE / LEUKOTRIENE SIGNALLING / LEUKOTRIENE BIOSYNTHESIS / MEMBRANE / EICOSANOID / TRANSMEMBRANE / MEMBRANE PROTEIN / APO / MAPEG / HUMAN / LTC4S / ENZYME / TRIMER
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
NICKEL (II) ION / PALMITIC ACID / Leukotriene C4 synthase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMartinez Molina, D. / Wetterholm, A. / Kohl, A. / McCarthy, A.A. / Niegowski, D. / Ohlson, E. / Hammarberg, T. / Eshaghi, S. / Haeggstrom, J.Z. / Nordlund, P.
CitationJournal: Nature / Year: 2007
Title: Structural Basis for Synthesis of Inflammatory Mediators by Human Leukotriene C4 Synthase.
Authors: Martinez Molina, D. / Wetterholm, A. / Kohl, A. / Mccarthy, A.A. / Niegowski, D. / Ohlson, E. / Hammarberg, T. / Eshaghi, S. / Haeggstrom, J.Z. / Nordlund, P.
History
DepositionMar 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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)22,39122
Polymers17,4121
Non-polymers4,97921
Water1,982110
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)67,17366
Polymers52,2353
Non-polymers14,93863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
Buried area13040 Å2
ΔGint-91.8 kcal/mol
Surface area29500 Å2
MethodPQS
Unit cell
Length a, b, c (Å)169.670, 169.670, 169.670
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-1151-

NI

21A-1152-

NI

31A-2003-

HOH

41A-2014-

HOH

51A-2034-

HOH

61A-2073-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein LEUKOTRIENE C4 SYNTHASE / / LEUKOTRIENE-C(4) SYNTHASE / LTC4 SYNTHASE


Mass: 17411.545 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZ / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: Q16873, leukotriene-C4 synthase
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 129 molecules

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


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 5.84 Å3/Da / Density % sol: 72.83 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.7→51.16 Å / Num. obs: 44247 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→28.27 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.98 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1376 5 %RANDOM
Rwork0.196 ---
obs0.198 25914 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.73 Å2
Refinement stepCycle: LAST / Resolution: 2→28.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 220 110 1538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211514
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.782.0752024
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9462054
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23415197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9621513
X-RAY DIFFRACTIONr_chiral_restr0.140.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021021
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.2723
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2966
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.2147
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1751.5827
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8121289
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7013753
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8454.5723
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 89 -
Rwork0.275 1882 -
obs--100 %

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