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- PDB-3d3l: The 2.6 A crystal structure of the lipoxygenase domain of human a... -

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Basic information

Entry
Database: PDB / ID: 3d3l
TitleThe 2.6 A crystal structure of the lipoxygenase domain of human arachidonate 12-lipoxygenase, 12S-type
ComponentsArachidonate 12-lipoxygenase, 12S-typeALOX12
KeywordsOXIDOREDUCTASE / ALOX12 / IRON-BINDING PROTEIN / ARACHIDONATE 12-LIPOXYGENASE / 12-LOX / PLATELET-TYPE LIPOXYGENASE 12 / OXYGENASE / ARACHIDONATE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Cytoplasm / Dioxygenase / Leukotriene biosynthesis / Metal-binding / Polymorphism
Function / homology
Function and homology information


unsaturated fatty acid metabolic process / hepoxilin-epoxide hydrolase activity / leukotriene A4 metabolic process / lipoxin B4 biosynthetic process / Synthesis of Hepoxilins (HX) and Trioxilins (TrX) / Biosynthesis of DPAn-6 SPMs / Hydrolases; Acting on ether bonds; Ether hydrolases / arachidonate 12-lipoxygenase / lipoxin A4 biosynthetic process / Biosynthesis of DHA-derived SPMs ...unsaturated fatty acid metabolic process / hepoxilin-epoxide hydrolase activity / leukotriene A4 metabolic process / lipoxin B4 biosynthetic process / Synthesis of Hepoxilins (HX) and Trioxilins (TrX) / Biosynthesis of DPAn-6 SPMs / Hydrolases; Acting on ether bonds; Ether hydrolases / arachidonate 12-lipoxygenase / lipoxin A4 biosynthetic process / Biosynthesis of DHA-derived SPMs / Biosynthesis of DPAn-3-derived maresins / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / arachidonate 12(S)-lipoxygenase activity / Synthesis of 12-eicosatetraenoic acid derivatives / linoleate 13S-lipoxygenase activity / Synthesis of Lipoxins (LX) / lipoxygenase pathway / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / arachidonic acid metabolic process / lipid oxidation / negative regulation of muscle cell apoptotic process / hepoxilin biosynthetic process / linoleic acid metabolic process / negative regulation of platelet aggregation / superoxide anion generation / fatty acid oxidation / establishment of skin barrier / sarcolemma / lipid metabolic process / iron ion binding / extracellular exosome / membrane / cytosol / cytoplasm
Similarity search - Function
Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase ...Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / 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. / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Nuclear Transport Factor 2; Chain: A, / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Polyunsaturated fatty acid lipoxygenase ALOX12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Svensson, L. / Thorsell, A.G. / Van Den Berg, S. / Welin, M. / Weigelt, J. / Wikstrom, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the lipoxygenase domain of human Arachidonate 12-lipoxygenase, 12S-type.
Authors: Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, ...Authors: Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Svensson, L. / Thorsell, A.G. / Van Den Berg, S. / Welin, M. / Weigelt, J. / Wikstrom, M. / Nordlund, P.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: database_2 / struct ...database_2 / struct / 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 / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arachidonate 12-lipoxygenase, 12S-type
B: Arachidonate 12-lipoxygenase, 12S-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4324
Polymers122,3202
Non-polymers1122
Water1,910106
1
A: Arachidonate 12-lipoxygenase, 12S-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2162
Polymers61,1601
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arachidonate 12-lipoxygenase, 12S-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2162
Polymers61,1601
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.590, 70.153, 77.868
Angle α, β, γ (deg.)65.37, 88.01, 69.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Arachidonate 12-lipoxygenase, 12S-type / ALOX12 / 12-LOX / Platelet-type lipoxygenase 12


Mass: 61160.129 Da / Num. of mol.: 2 / Fragment: Lipoxygenase domain: Residues 172-663 / Mutation: I663S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALOX12, LOG12 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: P18054, arachidonate 12-lipoxygenase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.0M LiCl2, 0.1M Citric acid pH 4.0, 20% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97627 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 30, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.6→47.193 Å / Num. all: 32115 / Num. obs: 31408 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.158 / Net I/σ(I): 10.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4642 / Rsym value: 0.509 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LOX

1lox


Resolution: 2.6→47.19 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.847 / SU B: 12.492 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 1.267 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 1628 5.1 %RANDOM
Rwork0.20625 ---
obs0.20976 30444 97.83 %-
all-31119 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.945 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.02 Å2-0.06 Å2
2---0.08 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.359 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 2 106 7268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227353
X-RAY DIFFRACTIONr_bond_other_d0.0010.025012
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.96610009
X-RAY DIFFRACTIONr_angle_other_deg0.968312240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6855890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86624.116328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.592151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1891542
X-RAY DIFFRACTIONr_chiral_restr0.1490.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021432
X-RAY DIFFRACTIONr_nbd_refined0.220.21924
X-RAY DIFFRACTIONr_nbd_other0.1870.25314
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23575
X-RAY DIFFRACTIONr_nbtor_other0.0880.23674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2227
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3650.27
X-RAY DIFFRACTIONr_mcbond_it0.5311.55817
X-RAY DIFFRACTIONr_mcbond_other0.0631.51768
X-RAY DIFFRACTIONr_mcangle_it0.6227288
X-RAY DIFFRACTIONr_scbond_it0.90733323
X-RAY DIFFRACTIONr_scangle_it1.3834.52721
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 141 -
Rwork0.305 2199 -
obs--97.18 %

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