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- PDB-3leo: Structure of human Leukotriene C4 synthase mutant R31Q in complex... -

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Basic information

Entry
Database: PDB / ID: 3leo
TitleStructure of human Leukotriene C4 synthase mutant R31Q in complex with glutathione
ComponentsLeukotriene C4 synthase
KeywordsLYASE / Leukotriene C4 synthase / Endoplasmic reticulum / Leukotriene biosynthesis / Membrane / Nucleus / Transmembrane
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
GLUTATHIONE / NICKEL (II) ION / PALMITOLEIC ACID / PALMITIC ACID / Leukotriene C4 synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsNiegowski, D. / Martinez-Molina, D. / Rinaldo-Matthis, A. / Nordlund, P. / Haeggstrom, J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Arginine 104 is a key catalytic residue in leukotriene C4 synthase.
Authors: Rinaldo-Matthis, A. / Wetterholm, A. / Martinez Molina, D. / Holm, J. / Niegowski, D. / Ohlson, E. / Nordlund, P. / Morgenstern, R. / Haeggstrom, J.Z.
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Non-polymer description
Revision 1.3Dec 26, 2012Group: Database references
Revision 1.4Sep 6, 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_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)20,51816
Polymers17,2511
Non-polymers3,26715
Water1,36976
1
A: Leukotriene C4 synthase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)246,218192
Polymers207,01512
Non-polymers39,203180
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation21_545y,z-1/2,x+1/21
crystal symmetry operation22_545-y,z-1/2,-x+1/21
crystal symmetry operation23_555y,-z+1/2,-x+1/21
crystal symmetry operation24_555-y,-z+1/2,x+1/21
crystal symmetry operation29_455z-1/2,x,y+1/21
crystal symmetry operation30_455z-1/2,-x,-y+1/21
crystal symmetry operation31_555-z+1/2,-x,y+1/21
crystal symmetry operation32_555-z+1/2,x,-y+1/21
Buried area112020 Å2
ΔGint-705 kcal/mol
Surface area65930 Å2
MethodPISA
2
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)61,55548
Polymers51,7543
Non-polymers9,80145
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation21_545y,z-1/2,x+1/21
crystal symmetry operation29_455z-1/2,x,y+1/21
Buried area21320 Å2
ΔGint-84 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.540, 169.540, 169.540
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-209-

SO4

21A-209-

SO4

31A-210-

NI

41A-211-

NI

51A-323-

HOH

61A-327-

HOH

71A-355-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 17251.283 Da / Num. of mol.: 1 / Mutation: R31Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: Q16873, leukotriene-C4 synthase
#7: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 7 types, 90 molecules

#2: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30O2
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2 M AmSO4, 0.1 M Bis-Tris, pH 6.5, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2008 / Details: Horizontally bended Ge(220)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 31399 / Num. obs: 31117 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 20.85
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.014 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.53 / % possible all: 91.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å37.91 Å
Translation2.1 Å37.91 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER1.3.3phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UUH

2uuh


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 5.699 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1201 5.1 %RANDOM
Rwork0.17163 ---
obs0.1729 22369 99.7 %-
all-23641 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.111 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 161 76 1420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211366
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8142.0471823
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8445149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50420.19252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64915178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0981512
X-RAY DIFFRACTIONr_chiral_restr0.1380.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02954
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.2594
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2906
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.621.5767
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.73421184
X-RAY DIFFRACTIONr_scbond_it4.4643664
X-RAY DIFFRACTIONr_scangle_it6.4964.5639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 94 -
Rwork0.171 1635 -
obs--100 %

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