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- PDB-4g32: Crystal Structure of a Phospholipid-Lipoxygenase Complex from Pse... -

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Basic information

Entry
Database: PDB / ID: 4g32
TitleCrystal Structure of a Phospholipid-Lipoxygenase Complex from Pseudomonas aeruginosa at 1.75A (P21212)
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 / lipid oxidation / 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: 1.75 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 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
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)76,99416
Polymers75,0541
Non-polymers1,94115
Water11,854658
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.696, 115.967, 42.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 3350, 50mM magnesium chloride, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 66015 / Num. obs: 66015 / % possible obs: 97.9 % / Redundancy: 3.9 % / Rsym value: 0.093 / Net I/σ(I): 10.7
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.5 % / Rsym value: 0.63 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FNQ (498-1066)

2fnq


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.847 / SU ML: 0.082 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21326 3322 5 %RANDOM
Rwork0.17906 ---
obs0.18078 62560 97.68 %-
all-65882 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.535 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20 Å2
2---0.15 Å20 Å2
3---0.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.204 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4851 0 126 658 5635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195122
X-RAY DIFFRACTIONr_bond_other_d0.0050.024968
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9856957
X-RAY DIFFRACTIONr_angle_other_deg1.1753.00511406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7145640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85123.014219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60915780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6031542
X-RAY DIFFRACTIONr_chiral_restr0.0880.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021163
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_it0.6090.9732530
X-RAY DIFFRACTIONr_mcbond_other0.610.9732529
X-RAY DIFFRACTIONr_mcangle_it0.9991.4553162
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0861.1612592
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 243 -
Rwork0.251 4440 -
obs--95.38 %
Refinement TLS params.Method: refined / Origin x: -30.5245 Å / Origin y: -12.1586 Å / Origin z: -18.0707 Å
111213212223313233
T0.0241 Å2-0.0034 Å20.0333 Å2-0.0035 Å2-0.0099 Å2--0.1146 Å2
L1.3011 °20.0189 °20.1031 °2-0.8954 °2-0.039 °2--0.3463 °2
S-0.0039 Å °-0.0521 Å °0.1202 Å °0.1087 Å °-0.0047 Å °0.0381 Å °-0.034 Å °0.0156 Å °0.0086 Å °

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