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- PDB-5ir4: Crystal structure of wild-type bacterial lipoxygenase from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 5ir4
TitleCrystal structure of wild-type bacterial lipoxygenase from Pseudomonas aeruginosa PA-LOX with space group C2221 at 1.48 A resolution
ComponentsArachidonate 15-lipoxygenaseALOX15
KeywordsOXIDOREDUCTASE / NON-HEME IRON ENZYME / PROTEIN-PHOSPHOLIPID COMPLEX / EICOSANOIDS / INFECTIOUS DISEASES
Function / homology
Function and homology information


arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / linoleate 13S-lipoxygenase activity / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid metabolic process / periplasmic space / extracellular region / 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
: / DI(HYDROXYETHYL)ETHER / Chem-ZPE / Lipoxygenase LoxA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsKalms, J. / Banthiya, S. / Galemou Yoga, E. / Kuhn, H. / Scheerer, P.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research FoundationUniCat - Research Field E3-1 Germany
German Research FoundationKu961/11-1 Germany
German Research FoundationGRK1673 Germany
German Research FoundationSFB740-B6 Germany
German Research FoundationSFB1078-B6 Germany
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Structural and functional basis of phospholipid oxygenase activity of bacterial lipoxygenase from Pseudomonas aeruginosa.
Authors: Banthiya, S. / Kalms, J. / Galemou Yoga, E. / Ivanov, I. / Carpena, X. / Hamberg, M. / Kuhn, H. / Scheerer, P.
History
DepositionMar 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arachidonate 15-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,60813
Polymers75,0541
Non-polymers1,55412
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-13 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.744, 97.391, 153.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-711-

MG

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Arachidonate 15-lipoxygenase / ALOX15 / 15-LOXm LINOLEATE 13-LIPOXYGENASE


Mass: 75053.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: loxA, PA1169 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I4G8*PLUS, linoleate 13S-lipoxygenase, EC: 1.13.11.13

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Non-polymers , 7 types, 564 molecules

#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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.2 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 12 % PEG 3350, 0.2 M MgCl2, 0.1 M TRIS pH 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2015 / Details: Mirror
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.48→48.97 Å / Num. obs: 104548 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.5
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G33

4g33


Resolution: 1.48→48.97 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.41 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15514 5276 5 %RANDOM
Rwork0.1358 ---
obs0.13677 99223 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å20 Å2
2---0.69 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.48→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5035 0 99 552 5686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195593
X-RAY DIFFRACTIONr_bond_other_d0.0020.025372
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9817640
X-RAY DIFFRACTIONr_angle_other_deg0.854312342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7025726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30122.988241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7915860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6281549
LS refinement shellResolution: 1.479→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 446 -
Rwork0.297 7076 -
obs--97.87 %
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)
10.19640.0327-0.06860.1299-0.03730.03640.0008-0.01380.00320.0108-0.0057-0.00880.0004-0.00060.00490.0131-0.0088-0.0020.01810.00190.004614.88626.0075-21.5849
21.52080.6217-1.34571.0743-0.23461.3123-0.02320.0423-0.12710.1765-0.0882-0.1140.1164-0.08590.11140.0621-0.0266-0.00190.02270.00920.02122.222513.6247-19.1775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 701
2X-RAY DIFFRACTION2A702

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