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- PDB-6lsv: Crystal structure of JOX2 in complex with 2OG, Fe, and JA -

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Basic information

Entry
Database: PDB / ID: 6lsv
TitleCrystal structure of JOX2 in complex with 2OG, Fe, and JA
ComponentsProbable 2-oxoglutarate-dependent dioxygenase At5g05600
KeywordsPLANT PROTEIN / jasmonic acid / 2OG oxygenase
Function / homology
Function and homology information


jasmonic acid hydrolase / response to karrikin / regulation of jasmonic acid mediated signaling pathway / flavonoid biosynthetic process / cellular response to toxic substance / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / dioxygenase activity / metal ion binding / cytosol
Similarity search - Function
Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Chem-JAA / Probable 2-oxoglutarate-dependent dioxygenase At5g05600
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsZhang, X. / Wang, D. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFD0300700 China
CitationJournal: Mol Plant / Year: 2021
Title: Structure-guided analysis of Arabidopsis JASMONATE-INDUCED OXYGENASE (JOX) 2 reveals key residues for recognition of jasmonic acid substrate by plant JOXs.
Authors: Zhang, X. / Wang, D. / Elberse, J. / Qi, L. / Shi, W. / Peng, Y.L. / Schuurink, R.C. / Van den Ackerveken, G. / Liu, J.
History
DepositionJan 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / Item: _citation.title
Revision 1.3May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable 2-oxoglutarate-dependent dioxygenase At5g05600
B: Probable 2-oxoglutarate-dependent dioxygenase At5g05600
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0678
Polymers80,2422
Non-polymers8246
Water2,342130
1
A: Probable 2-oxoglutarate-dependent dioxygenase At5g05600
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5334
Polymers40,1211
Non-polymers4123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area14780 Å2
MethodPISA
2
B: Probable 2-oxoglutarate-dependent dioxygenase At5g05600
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5334
Polymers40,1211
Non-polymers4123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.476, 74.416, 75.488
Angle α, β, γ (deg.)90.000, 110.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable 2-oxoglutarate-dependent dioxygenase At5g05600


Mass: 40121.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g05600, MOP10.14 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FFF6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-JAA / {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid / Jasmonic acid


Mass: 210.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Chemical ChemComp-FE / FE (III) ION / Iron


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


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES, pH 7.5, 1.26M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 23124 / % possible obs: 98.96 % / Redundancy: 6.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.054 / Net I/σ(I): 16.1
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 7 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 2225 / CC1/2: 0.934 / Rpim(I) all: 0.193 / % possible all: 96.49

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIX1.14rc2_3191: ???phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GP4
Resolution: 2.651→26.334 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1137 4.92 %
Rwork0.1951 21978 -
obs0.197 23115 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.81 Å2 / Biso mean: 33.0983 Å2 / Biso min: 15.18 Å2
Refinement stepCycle: final / Resolution: 2.651→26.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 52 130 5624
Biso mean--31.24 33.07 -
Num. residues----676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.651-2.77120.29961560.2253263196
2.7712-2.91710.27911330.2185272699
2.9171-3.09960.22861230.2145277499
3.0996-3.33850.26281320.2082274099
3.3385-3.67370.21021430.18922754100
3.6737-4.20340.20841510.18322775100
4.2034-5.28880.21871460.16592786100
5.2888-26.3340.23881530.206279299

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