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Basic information

Entry
Database: PDB / ID: 3rde
TitleCrystal structure of the catalytic domain of porcine leukocyte 12-lipoxygenase
ComponentsArachidonate 12-lipoxygenase, 12S-type
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / lipoxygenase / C-terminal domain / protein-inhibitor complex / 4-(2-oxapentadeca-4-yne)phenylpropanoic acid / lipoxygenase catalytic domain / dioxygenase / Fe / leukocyte / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


cellular response to interleukin-13 / regulation of engulfment of apoptotic cell / negative regulation of adaptive immune response / regulation of peroxisome proliferator activated receptor signaling pathway / arachidonate 12-lipoxygenase / lipoxin A4 biosynthetic process / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / arachidonate 12(S)-lipoxygenase activity / linoleate 13S-lipoxygenase ...cellular response to interleukin-13 / regulation of engulfment of apoptotic cell / negative regulation of adaptive immune response / regulation of peroxisome proliferator activated receptor signaling pathway / arachidonate 12-lipoxygenase / lipoxin A4 biosynthetic process / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / arachidonate 12(S)-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / phosphatidylethanolamine biosynthetic process / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / lipoxygenase pathway / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / linoleic acid metabolic process / apoptotic cell clearance / positive regulation of cell-substrate adhesion / positive regulation of actin filament polymerization / bone mineralization / fatty acid oxidation / extrinsic component of cytoplasmic side of plasma membrane / cellular response to calcium ion / phosphatidylinositol-4,5-bisphosphate binding / response to endoplasmic reticulum stress / lipid droplet / ossification / wound healing / lipid metabolic process / regulation of inflammatory response / positive regulation of ERK1 and ERK2 cascade / iron ion binding / membrane / plasma membrane / cytosol
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
: / : / Chem-OYP / Polyunsaturated fatty acid lipoxygenase ALOX15
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.892 Å
AuthorsFunk, M.O. / Xu, S. / Marnett, L.J. / Mueser, T.C.
CitationJournal: Structure / Year: 2012
Title: Crystal structure of 12-lipoxygenase catalytic-domain-inhibitor complex identifies a substrate-binding channel for catalysis.
Authors: Xu, S. / Mueser, T.C. / Marnett, L.J. / Funk, M.O.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Aug 1, 2012Group: Database references
Revision 1.3Sep 26, 2012Group: Database references
Revision 1.4Sep 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_conn.ptnr2_label_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)260,80114
Polymers259,0654
Non-polymers1,73610
Water22,9511274
1
A: Arachidonate 12-lipoxygenase, 12S-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2204
Polymers64,7661
Non-polymers4533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arachidonate 12-lipoxygenase, 12S-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1813
Polymers64,7661
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Arachidonate 12-lipoxygenase, 12S-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1813
Polymers64,7661
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Arachidonate 12-lipoxygenase, 12S-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2204
Polymers64,7661
Non-polymers4533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-48 kcal/mol
Surface area79990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.450, 181.540, 91.610
Angle α, β, γ (deg.)90.00, 92.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 64766.227 Da / Num. of mol.: 4 / Fragment: unp residues 112-663 / Mutation: C210S C292S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ALOX12 / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 Cell (DE3) / References: UniProt: P16469, arachidonate 12-lipoxygenase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-OYP / 3-{4-[(tridec-2-yn-1-yloxy)methyl]phenyl}propanoic acid


Mass: 358.514 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H34O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1274 / 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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: protein 6 mg/mL incubated with the solid OPP inhibitor for 16 hours, then further concentrated to 11~12 mg/mL in 10 mM Tris HCl, 1 mM TCEP, pH 7.4 buffer. reservoir solution: 0.1 M MES pH 6. ...Details: protein 6 mg/mL incubated with the solid OPP inhibitor for 16 hours, then further concentrated to 11~12 mg/mL in 10 mM Tris HCl, 1 mM TCEP, pH 7.4 buffer. reservoir solution: 0.1 M MES pH 6.5, 5%-10% PEG-20,000, 20% glycerol against 1 mL well solution of 0.1 M MES, 5%-10% PEG-20,000, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2011
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.89→48.968 Å / Num. all: 214779 / Num. obs: 214779 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.098 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.89-1.993.40.2842.40.284198.3
1.99-2.123.40.23.40.2198.9
2.12-2.263.50.164.10.16199.4
2.26-2.443.60.12750.127199.8
2.44-2.683.70.1155.40.1151100
2.68-2.993.80.0976.30.0971100
2.99-3.453.90.0966.10.0961100
3.45-4.233.90.0817.40.0811100
4.23-5.983.90.078.10.071100
5.98-48.9683.80.0658.30.065199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.8 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.97 Å
Translation2.5 Å48.97 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P0M

2p0m


Resolution: 1.892→48.968 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.1223 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.124
Stereochemistry target values: MAXIMUM LIKELIHOOD DATA USED IN REFINEMENT.
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21447 6468 3 %RANDOM
Rwork0.17195 ---
obs0.17323 214717 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.665 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.05 Å2
2---0.17 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.892→48.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17580 0 110 1274 18964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02218091
X-RAY DIFFRACTIONr_bond_other_d00.0212506
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.97424549
X-RAY DIFFRACTIONr_angle_other_deg4.113330451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09752208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67823.667818
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14153097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.43815129
X-RAY DIFFRACTIONr_chiral_restr0.1370.22710
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02119909
X-RAY DIFFRACTIONr_gen_planes_other0.0170.023666
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_it1.3371.511013
X-RAY DIFFRACTIONr_mcbond_other01.54403
X-RAY DIFFRACTIONr_mcangle_it2.244217788
X-RAY DIFFRACTIONr_scbond_it3.47537078
X-RAY DIFFRACTIONr_scangle_it5.3044.56754
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.892→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 509 -
Rwork0.213 15192 -
obs--98 %

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