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- PDB-5ir5: Crystal structure of wild-type bacterial lipoxygenase from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 5ir5
TitleCrystal structure of wild-type bacterial lipoxygenase from Pseudomonas aeruginosa PA-LOX with space group P21212 at 1.9 A resolution
ComponentsArachidonate 15-lipoxygenase
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
: / Chem-ZPE / Lipoxygenase LoxA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 FoundationGRK1673 Germany
German Research FoundationKu961/11-1 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)76,0977
Polymers75,0541
Non-polymers1,0436
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-12 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.093, 116.353, 42.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Arachidonate 15-lipoxygenase / 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: IOMTU133_4416 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I4G8*PLUS, linoleate 13S-lipoxygenase, arachidonate 15-lipoxygenase

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Non-polymers , 5 types, 477 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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.4 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10 % PEG 3350, 50 mM MgCl2, 100 mM HEPES, pH 7.5

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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: 1.9→43.8 Å / Num. obs: 53115 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G32

4g32


Resolution: 1.9→43.8 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 7.331 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18195 2586 4.9 %RANDOM
Rwork0.14408 ---
obs0.14593 50471 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.388 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å2-0 Å2
2---0.44 Å2-0 Å2
3---2 Å2
Refinement stepCycle: 1 / Resolution: 1.9→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4804 0 67 471 5342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195086
X-RAY DIFFRACTIONr_bond_other_d0.0020.024901
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9796937
X-RAY DIFFRACTIONr_angle_other_deg0.859311241
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 193 -
Rwork0.241 3704 -
obs--99.72 %
Refinement TLS params.Method: refined / Origin x: 30.688 Å / Origin y: 12.3385 Å / Origin z: 3.1566 Å
111213212223313233
T0.0358 Å2-0.0007 Å2-0.005 Å2-0.0005 Å20.0005 Å2--0.1202 Å2
L0.1099 °20.0108 °2-0.0125 °2-0.1145 °20.0125 °2--0.0031 °2
S-0.0005 Å °0.0002 Å °-0.0148 Å °0.0138 Å °-0.0002 Å °-0.0072 Å °0.002 Å °-0.0002 Å °0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 701
2X-RAY DIFFRACTION1A702

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