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- PDB-9lby: Crystal Structure of Maize Lipoxygenase3 -

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Basic information

Entry
Database: PDB / ID: 9lby
TitleCrystal Structure of Maize Lipoxygenase3
ComponentsLipoxygenase
KeywordsOXIDOREDUCTASE / lipoxygenase / LA / susceptibility factor
Function / homology
Function and homology information


linoleate 9S-lipoxygenase / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / response to other organism / response to wounding / fatty acid biosynthetic process / metal ion binding
Similarity search - Function
Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / 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, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / 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.
Similarity search - Domain/homology
: / linoleate 9S-lipoxygenase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsZhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of Maize Lipoxygenase3
Authors: Zhang, X.
History
DepositionJan 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Lipoxygenase
A: Lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5144
Polymers195,4032
Non-polymers1122
Water25,3831409
1
B: Lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7572
Polymers97,7011
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-14 kcal/mol
Surface area31790 Å2
MethodPISA
2
A: Lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7572
Polymers97,7011
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-14 kcal/mol
Surface area31380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.510, 75.040, 107.720
Angle α, β, γ (deg.)98.91, 101.88, 113.71
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lipoxygenase


Mass: 97701.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 542495, ZEAMMB73_Zm00001d033623 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8W0V2
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 1409 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 50.48 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH5.5,25% w/v Polyethylene glycol 3,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.08→27.36 Å / Num. obs: 109557 / % possible obs: 96.96 % / Redundancy: 6 % / CC1/2: 0.993 / Net I/σ(I): 7.3
Reflection shellResolution: 2.08→9.3 Å / Num. unique obs: 10884 / CC1/2: 0.636

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→27.36 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 5265 4.81 %
Rwork0.197 --
obs0.1992 109530 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12928 0 2 1409 14339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913257
X-RAY DIFFRACTIONf_angle_d1.08218040
X-RAY DIFFRACTIONf_dihedral_angle_d14.3011790
X-RAY DIFFRACTIONf_chiral_restr0.0611964
X-RAY DIFFRACTIONf_plane_restr0.0072351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.10.34881930.29613413X-RAY DIFFRACTION96
2.1-2.130.31531630.27813468X-RAY DIFFRACTION96
2.13-2.150.30061660.27023479X-RAY DIFFRACTION97
2.15-2.180.28681840.2543482X-RAY DIFFRACTION97
2.18-2.210.27371920.2573432X-RAY DIFFRACTION97
2.21-2.240.33631840.25123471X-RAY DIFFRACTION97
2.24-2.270.29651650.25533478X-RAY DIFFRACTION96
2.27-2.310.29911920.24623464X-RAY DIFFRACTION97
2.31-2.340.29151800.23243492X-RAY DIFFRACTION97
2.34-2.380.27841590.23733486X-RAY DIFFRACTION97
2.38-2.420.27741670.22783479X-RAY DIFFRACTION97
2.42-2.470.26011550.22223520X-RAY DIFFRACTION97
2.47-2.510.25581670.2263490X-RAY DIFFRACTION98
2.51-2.560.27511740.21823483X-RAY DIFFRACTION97
2.56-2.620.2691740.21253482X-RAY DIFFRACTION98
2.62-2.680.26232070.21713498X-RAY DIFFRACTION98
2.68-2.750.24621760.21653480X-RAY DIFFRACTION97
2.75-2.820.27851650.21393492X-RAY DIFFRACTION97
2.82-2.910.28921720.21613513X-RAY DIFFRACTION98
2.91-30.28071790.21383524X-RAY DIFFRACTION98
3-3.110.25961480.20953450X-RAY DIFFRACTION97
3.11-3.230.26051660.19923418X-RAY DIFFRACTION96
3.23-3.380.24171550.18933522X-RAY DIFFRACTION97
3.38-3.550.24451790.18263524X-RAY DIFFRACTION98
3.55-3.780.21311940.1663480X-RAY DIFFRACTION98
3.78-4.070.1971880.15673474X-RAY DIFFRACTION98
4.07-4.480.17911700.14513478X-RAY DIFFRACTION97
4.48-5.120.19421630.14313439X-RAY DIFFRACTION96
5.12-6.430.19741920.17363500X-RAY DIFFRACTION97
6.44-27.360.19361960.17643354X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6821-0.006-0.34211.43740.41141.7185-0.06820.0208-0.0934-0.15390.0237-0.15970.32290.07160.03020.3288-0.05770.00240.16010.01770.20637.0874-59.505615.8323
21.15040.7425-0.26591.3516-0.31480.81190.0874-0.0683-0.10780.1445-0.0987-0.1521-0.07220.11080.03060.2406-0.0436-0.00490.1651-0.00140.153447.6096-36.207621.3017
32.6157-0.46440.3811.942-0.45592.0014-0.01030.3951-0.2553-0.2897-0.0039-0.33290.02550.46020.01270.3524-0.0260.06910.3454-0.0430.269961.3325-20.3674-8.5982
40.72730.3893-0.191.4343-0.53090.57170.02560.01850.09110.03320.01530.1418-0.0571-0.0392-0.0480.1793-0.01120.01130.1572-0.03040.130137.0939-12.29039.6043
51.6883-0.8973-0.04430.54890.38891.7772-0.0830.43790.2097-0.32710.1312-0.4132-0.30870.2852-0.02310.2995-0.04710.04490.29720.0140.173654.1316-6.366-4.0971
61.51050.5815-0.23380.9546-0.21371.0285-0.09290.204-0.0771-0.28150.0950.12980.063-0.10390.00020.3306-0.0364-0.03330.2233-0.03090.194435.223-28.7955-3.0145
71.3396-0.26070.18951.9318-0.45541.4036-0.03320.0713-0.0552-0.0363-0.0838-0.4396-0.06180.24550.13260.3126-0.12550.01110.26630.03080.272681.0131-14.1478-55.0213
80.62240.13790.141.51980.02621.2042-0.09010.0964-0.1555-0.38260.128-0.21780.20630.1068-0.01960.3062-0.04960.04160.2361-0.0220.190264.5154-37.1584-58.3259
90.94230.11040.5721.3427-0.30151.44080.1970.034-0.2603-0.0624-0.0642-0.34820.43110.2708-0.11790.42820.0163-0.0480.26440.00520.333664.6053-59.2457-33.1787
101.0744-0.26830.34741.214-0.17360.78580.1706-0.3456-0.24120.1289-0.01620.17060.353-0.4018-0.11660.3934-0.1714-0.03980.42050.09910.296242.1931-56.0308-29.6159
110.61360.30160.19691.1767-0.18170.99280.0374-0.0707-0.06220.03990.03040.03380.1017-0.1126-0.06210.231-0.04880.01330.1978-0.00420.13753.616-38.8476-37.4285
121.4016-0.8542-0.08410.97560.26220.9646-0.0452-0.058-0.59560.1990.16590.00880.5842-0.0106-0.11350.4998-0.015-0.05820.22510.02580.322959.9913-63.1474-33.122
130.71360.03850.10141.91560.43621.64380.0746-0.0751-0.01380.16940.0109-0.1429-0.060.2156-0.07550.2394-0.0447-0.02510.2831-0.00540.206670.4594-36.512-30.254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 16 through 145 )
2X-RAY DIFFRACTION2chain 'B' and (resid 146 through 281 )
3X-RAY DIFFRACTION3chain 'B' and (resid 282 through 360 )
4X-RAY DIFFRACTION4chain 'B' and (resid 361 through 706 )
5X-RAY DIFFRACTION5chain 'B' and (resid 707 through 760 )
6X-RAY DIFFRACTION6chain 'B' and (resid 761 through 864 )
7X-RAY DIFFRACTION7chain 'A' and (resid 16 through 169 )
8X-RAY DIFFRACTION8chain 'A' and (resid 170 through 281 )
9X-RAY DIFFRACTION9chain 'A' and (resid 282 through 390 )
10X-RAY DIFFRACTION10chain 'A' and (resid 391 through 449 )
11X-RAY DIFFRACTION11chain 'A' and (resid 450 through 706 )
12X-RAY DIFFRACTION12chain 'A' and (resid 707 through 760 )
13X-RAY DIFFRACTION13chain 'A' and (resid 761 through 864 )

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