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- PDB-1rov: Lipoxygenase-3 Treated with Cumene Hydroperoxide -

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Basic information

Entry
Database: PDB / ID: 1rov
TitleLipoxygenase-3 Treated with Cumene Hydroperoxide
ComponentsSeed lipoxygenase-3
KeywordsOXIDOREDUCTASE / BETA HYDROXYLATION
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
: / Seed linoleate 9S-lipoxygenase-3
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVahedi-Faridi, A. / Brault, P.A. / Shah, P. / Kim, Y.W. / Dunham, W.R. / Funk, M.O.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Interaction between non-heme iron of lipoxygenases and cumene hydroperoxide: basis for enzyme activation, inactivation, and inhibition
Authors: Vahedi-Faridi, A. / Brault, P.A. / Shah, P. / Kim, Y.W. / Dunham, W.R. / Funk, M.O.
History
DepositionDec 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Seed lipoxygenase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0072
Polymers96,9511
Non-polymers561
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.001, 136.901, 61.512
Angle α, β, γ (deg.)90.00, 96.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Seed lipoxygenase-3 / L-3


Mass: 96951.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Strain: L. Merrill cv Resnick / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.48 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: PEG 8000,sodium citrate-phosphate, sodium phosphate , pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris-HCl1droppH7.0
210 mg/mlprotein1drop
320 %(v/v)PEG80001reservoir
40.05 Msodium citrate phosphate1reservoirpH4.6
50.1 Msodium phosphate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2003 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.37 Å / Num. all: 61477 / Num. obs: 48034 / % possible obs: 78.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.054 / Net I/σ(I): 15.9
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.217 / % possible all: 75.5
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. obs: 50653 / % possible obs: 83 % / Redundancy: 2.4 % / Num. measured all: 109207 / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.37 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2419 -RANDOM
Rwork0.221 ---
all0.221 48034 --
obs0.221 48034 78 %-
Solvent computationBsol: 21.4129 Å2 / ksol: 0.329691 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.617 Å20 Å2-5.375 Å2
2--1.5 Å20 Å2
3---5.117 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 1 301 7000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_angle_deg3.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_improper_angle_d4.03
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.257 365 -
Rwork0.257 --
obs--67.2 %
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.2213 / Rfactor Rwork: 0.2147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.03

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