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- PDB-4nta: Mus Musculus LTC4 synthase in apo form -

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Basic information

Entry
Database: PDB / ID: 4nta
TitleMus Musculus LTC4 synthase in apo 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 / leukotriene biosynthetic process ...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 / leukotriene biosynthetic process / nuclear outer membrane / enzyme activator activity / lipid metabolic process / nuclear envelope / transferase activity / nuclear membrane / lipid binding / endoplasmic reticulum 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
PALMITIC ACID / Leukotriene C4 synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsNiegowski, D. / Rinaldo-Matthis, A. / Haeggstrom, J.Z.
CitationJournal: To be Published
Title: Mus Musculus LTC4 synthase in apo form
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)18,8767
Polymers17,6581
Non-polymers1,2186
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)56,62721
Polymers52,9743
Non-polymers3,65318
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 area10350 Å2
ΔGint-75 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.575, 169.575, 169.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23

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Components

#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
#2: Chemical
ChemComp-PLM / PALMITIC ACID


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 5.75 Å3/Da / Density % sol: 78.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.3
Details: 1.9 M NH4SO4, 0.2 M NaCl, 0.1 M Na-cacadylate, pH 6.3, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.999→97.959 Å / Num. all: 11165 / Num. obs: 11165 / % possible obs: 99.5 % / Observed criterion σ(F): 2.092 / Redundancy: 3.3 % / Biso Wilson estimate: 85.54 Å2 / Rsym value: 0.046 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.852.90.8170.9464316250.81799
2.85-3.023.50.5181.4538015220.51899.8
3.02-3.233.40.3242.2494714440.32499.9
3.23-3.493.40.154.8455213430.1599.7
3.49-3.823.50.0749.7425212240.07499.5
3.82-4.273.30.04315.1379911350.04399.7
4.27-4.933.50.03319.334599900.03399.6
4.93-6.043.40.03319.328228400.03399.5
6.04-8.543.40.02820.122546700.02899.3
8.54-42.3943.30.038.212093720.0398.5

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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: PDB entry 2UUI

2uui


Resolution: 2.7→42.394 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7752 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 550 4.93 %R-Free flag copied from PDB ID 2UUI: Random
Rwork0.2287 ---
obs0.2302 11160 99.32 %-
all-11165 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 264.04 Å2 / Biso mean: 83.5864 Å2 / Biso min: 28.49 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 48 0 1224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011261
X-RAY DIFFRACTIONf_angle_d1.2841705
X-RAY DIFFRACTIONf_chiral_restr0.099188
X-RAY DIFFRACTIONf_plane_restr0.008206
X-RAY DIFFRACTIONf_dihedral_angle_d17.507446
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7002-2.97190.2981460.26852615276199
2.9719-3.40170.32561350.249726312766100
3.4017-4.28520.25631240.216626752799100
4.2852-42.3990.24181450.22592689283499
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)
10.0022-0.00030.0010.0001-0.00060.0021-0.00350.01770.01450.0137-0.0034-0.0007-0.0006-0.022300.74590.1343-0.03810.78810.15440.606913.4939-3.7964-77.3592
20.0171-0.0753-0.05450.35590.00990.11030.0924-0.2742-0.09590.5927-0.0076-0.56450.01170.20680.14370.22150.3979-0.63490.22840.30650.405424.2358-13.3508-56.7147
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 145 )A0

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