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- PDB-4g33: Crystal Structure of a Phospholipid-Lipoxygenase Complex from Pse... -

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Basic information

Entry
Database: PDB / ID: 4g33
TitleCrystal Structure of a Phospholipid-Lipoxygenase Complex from Pseudomonas aeruginosa at 2.0 A (C2221)
Components15S-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-ZPE / Linoleate 9/13-lipoxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsCarpena, X. / Garreta, A. / Val-Moraes, S.P. / Garcia-Fernandez, Q. / Fita, I.
CitationJournal: Faseb J. / Year: 2013
Title: Structure and interaction with phospholipids of a prokaryotic lipoxygenase from Pseudomonas aeruginosa.
Authors: Garreta, A. / Val-Moraes, S.P. / Garcia-Fernandez, Q. / Busquets, M. / Juan, C. / Oliver, A. / Ortiz, A. / Gaffney, B.J. / Fita, I. / Manresa, A. / Carpena, X.
History
DepositionJul 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: 15S-LIPOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2588
Polymers75,0541
Non-polymers1,2047
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 15S-LIPOXYGENASE
hetero molecules

A: 15S-LIPOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,51516
Polymers150,1072
Non-polymers2,40814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area12110 Å2
ΔGint-105 kcal/mol
Surface area47410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.850, 97.276, 157.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 15S-LIPOXYGENASE / LINOLEATE LIPOXYGENASE


Mass: 75053.500 Da / Num. of mol.: 1
Fragment: Secretable Pa_LOX without the periplasmic signal peptide
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
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZPE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradec-5-enoyloxy)propyl (11Z)-octadec-11-enoate


Mass: 687.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H70NO8P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPHOSPHATIDYLETHANOLAMINE PHOSPHOLIPID HAS FATTY ACID CHAINS OF 18 (SN1) AND 14/16 (SN2) CARBON ...PHOSPHATIDYLETHANOLAMINE PHOSPHOLIPID HAS FATTY ACID CHAINS OF 18 (SN1) AND 14/16 (SN2) CARBON ATOMS IN LENGTH.

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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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG 3350, 0.2M MgCl2, 0.1M TRIS pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 42120 / Num. obs: 42120 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 27.81 Å2 / Rsym value: 0.109 / Net I/σ(I): 9
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.648 / % possible all: 94.9

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Processing

Software
NameVersionClassification
ProDCdata collection
MOLREPphasing
REFMACrefinement
BUSTER2.10.0refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G32

4g32


Resolution: 2.03→19.84 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9185 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 2164 5.21 %RANDOM
Rwork0.1801 ---
obs0.1824 41570 98.35 %-
all-41570 --
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.0539 Å20 Å20 Å2
2--10.1872 Å20 Å2
3----12.2411 Å2
Refine analyzeLuzzati coordinate error obs: 0.335 Å
Refinement stepCycle: LAST / Resolution: 2.03→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5095 0 78 243 5416
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095312HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.037223HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1809SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes116HARMONIC2
X-RAY DIFFRACTIONt_gen_planes783HARMONIC5
X-RAY DIFFRACTIONt_it5312HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion17.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion674SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6417SEMIHARMONIC4
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2716 151 5.23 %
Rwork0.2201 2737 -
all0.223 2888 -
obs--98.35 %
Refinement TLS params.Method: refined / Origin x: -15.5247 Å / Origin y: -25.5076 Å / Origin z: -22.0229 Å
111213212223313233
T-0.0244 Å2-0.0022 Å2-0.0932 Å2--0.0843 Å20.0307 Å2--0.0683 Å2
L1.6418 °20.7546 °20.3513 °2-1.7952 °2-0.0143 °2--0.6344 °2
S0.0036 Å °-0.1048 Å °-0.3612 Å °0.0045 Å °0.0016 Å °-0.3537 Å °-0.0755 Å °-0.0406 Å °-0.0051 Å °
Refinement TLS groupSelection details: { A|* }

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