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- PDB-4rpe: Crystal Structure of Variant G186E from Pseudomonas Aeruginosa Li... -

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Basic information

Entry
Database: PDB / ID: 4rpe
TitleCrystal Structure of Variant G186E from Pseudomonas Aeruginosa Lipoxygenase 2 at 1.60A (C2)
ComponentsLinoleate 9/13-lipoxygenase
KeywordsOXIDOREDUCTASE / non-heme iron enzyme / protein-phospholipid complex
Function / homology
Function and homology information


oleate 10S-lipoxygenase / linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / lipoxygenase pathway / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process ...oleate 10S-lipoxygenase / linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / lipoxygenase pathway / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / periplasmic space / metal ion binding
Similarity search - Function
Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile.
Similarity search - Domain/homology
Chem-8PE / : / Linoleate 9/13-lipoxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCarpena, X. / Garreta, A. / Herrero, L. / Fita, I.
CitationJournal: To be Published
Title: Crystal Structure of Lipoxygenase 2 in space group C2
Authors: Carpena, X. / Garreta, A. / Herrero, L. / Fita, I.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_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: Linoleate 9/13-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8733
Polymers75,1261
Non-polymers7482
Water8,611478
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Linoleate 9/13-lipoxygenase
hetero molecules

A: Linoleate 9/13-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,7476
Polymers150,2512
Non-polymers1,4964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5240 Å2
ΔGint-53 kcal/mol
Surface area47880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.630, 96.880, 87.320
Angle α, β, γ (deg.)90.00, 107.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Linoleate 9/13-lipoxygenase / Oleate 10S-lipoxygenase / 15S-Lipoxygenase


Mass: 75125.570 Da / Num. of mol.: 1
Fragment: secretable Pa_LOX without the periplasmic signal peptide (UNP residues 19-685)
Mutation: G186E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lox / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RNT4, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen, linoleate 9S-lipoxygenase, oleate 10S-lipoxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-8PE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG, pH 7.5, VAPOR DIFFUSION, HANGING 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 4 / Detector: CCD
RadiationMonochromator: diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.6→19.84 Å / Num. all: 88460 / Num. obs: 84566 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.6 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.8.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.84 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.881 / SU B: 2.748 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 4253 5 %RANDOM
Rwork0.22671 ---
all0.22902 80313 --
obs0.22902 80313 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0 Å2-0.5 Å2
2---0.38 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 46 478 5602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195457
X-RAY DIFFRACTIONr_bond_other_d0.0010.025290
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.9797469
X-RAY DIFFRACTIONr_angle_other_deg0.9823.00412168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.295709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.923.176233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84615863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7851544
X-RAY DIFFRACTIONr_chiral_restr0.1180.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021249
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.351.5752735
X-RAY DIFFRACTIONr_mcbond_other1.351.5752734
X-RAY DIFFRACTIONr_mcangle_it1.8892.3653449
X-RAY DIFFRACTIONr_mcangle_other1.8882.3653450
X-RAY DIFFRACTIONr_scbond_it1.6721.7132721
X-RAY DIFFRACTIONr_scbond_other1.6711.7132722
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4682.5094010
X-RAY DIFFRACTIONr_long_range_B_refined4.57313.3756827
X-RAY DIFFRACTIONr_long_range_B_other4.42813.1426643
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 290 -
Rwork0.312 5857 -
obs--94.71 %

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