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- PDB-1no3: REFINED STRUCTURE OF SOYBEAN LIPOXYGENASE-3 WITH 4-NITROCATECHOL ... -

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Basic information

Entry
Database: PDB / ID: 1no3
TitleREFINED STRUCTURE OF SOYBEAN LIPOXYGENASE-3 WITH 4-NITROCATECHOL AT 2.15 ANGSTROM RESOLUTION
ComponentsLipoxygenase-3
KeywordsOXIDOREDUCTASE / lipoxygenase / 4-nitrocatechol / iron
Function / homology
Function and homology information


linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Lipoxygenase-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 ...Lipoxygenase-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase-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, / Few Secondary Structures / Irregular / Roll / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-NITROCATECHOL / : / Seed linoleate 9S-lipoxygenase-3
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSkrzypczak-Jankun, E. / Borbulevych, O.Y. / Jankun, J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Soybean lipoxygenase-3 in complex with 4-nitrocatechol.
Authors: Skrzypczak-Jankun, E. / Borbulevych, O.Y. / Jankun, J.
#1: Journal: Biochemistry / Year: 1998
Title: Structural and thermochemical characterization of Lipoxygenase-catechol complexes
Authors: Pham, C. / Jankun, J. / Skrzypczak-Jankun, E. / Flowers, R.A. / Funk Jr., M.O.
History
DepositionJan 15, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionJun 3, 2003ID: 1BYT
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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_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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_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: Lipoxygenase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1303
Polymers96,9191
Non-polymers2112
Water8,899494
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.905, 137.531, 61.880
Angle α, β, γ (deg.)90.00, 95.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1504-

HOH

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Components

#1: Protein Lipoxygenase-3


Mass: 96919.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Strain: Resnick Cultivar / References: UniProt: P09186, linoleate 13S-lipoxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-4NC / 4-NITROCATECHOL


Mass: 155.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 20% PEG 8000, citrate-phosphate buffer 0.05M, tris.HCl, 0.2% sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: Focusing mirrors
RadiationMonochromator: Focussing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 50978 / Num. obs: 50343 / % possible obs: 0.988 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 34.02 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.7
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.14 / Num. unique all: 5046 / % possible all: 0.993
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 49989 / % possible obs: 99.1 %
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
CCP4V. 4.2.1 (MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BYT

1byt
PDB Unreleased entry


Resolution: 2.15→10 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.532 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic thermal model / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 2543 5.1 %RANDOM
Rwork0.1863 ---
all0.1887 49989 --
obs0.1887 47446 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20.97 Å2
2--0.63 Å20 Å2
3----1.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.26 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6799 0 12 494 7305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216998
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.9559502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4515852
X-RAY DIFFRACTIONr_chiral_restr0.130.21035
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025368
X-RAY DIFFRACTIONr_nbd_refined0.1610.072990
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.4637
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.0749
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.413
X-RAY DIFFRACTIONr_mcbond_it0.9291.54254
X-RAY DIFFRACTIONr_mcangle_it1.65226897
X-RAY DIFFRACTIONr_scbond_it2.90232744
X-RAY DIFFRACTIONr_scangle_it4.1634.52605
LS refinement shellResolution: 2.15→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 170 -
Rwork0.225 3394 -
obs-3394 0.992 %
Refinement TLS params.Method: refined / Origin x: 27.5675 Å / Origin y: 4.0796 Å / Origin z: 15.6647 Å
111213212223313233
T0.0146 Å20.0312 Å2-0.0271 Å2-0.0694 Å2-0.0554 Å2--0.0528 Å2
L0.988 °20.355 °2-0.3657 °2-1.5 °2-0.3657 °2--1.525 °2
S0.0003 Å °0.0128 Å °-0.0089 Å °0.0492 Å °0.0576 Å °0.1227 Å °-0.0064 Å °-0.1604 Å °-0.0579 Å °
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.979
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg7.451

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