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- PDB-6ip0: Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain ... -

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Basic information

Entry
Database: PDB / ID: 6ip0
TitleCrystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with AKG
ComponentsTranscription factor jumonji (Jmj) family protein
KeywordsGENE REGULATION / Arabidopsis / histone modification / flowering / epigenetics / H3K27me3
Function / homology
Function and homology information


negative regulation of short-day photoperiodism, flowering / long-day photoperiodism / negative regulation of long-day photoperiodism, flowering / histone H3K27me2/H3K27me3 demethylase activity / flower development / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / 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 / negative regulation of gene expression, epigenetic / response to temperature stimulus / histone demethylase activity ...negative regulation of short-day photoperiodism, flowering / long-day photoperiodism / negative regulation of long-day photoperiodism, flowering / histone H3K27me2/H3K27me3 demethylase activity / flower development / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / 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 / negative regulation of gene expression, epigenetic / response to temperature stimulus / histone demethylase activity / histone binding / chromatin remodeling / DNA-binding transcription factor activity / regulation of DNA-templated transcription / metal ion binding / nucleus
Similarity search - Function
Zinc finger, C5HC2-type / C5HC2 zinc finger / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NICKEL (II) ION / Transcription factor jumonji (Jmj) family protein / zinc finger (C5HC2 type) family protein / Lysine-specific demethylase JMJ13
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsHu, H. / Du, J.
CitationJournal: Nat Commun / Year: 2019
Title: The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor.
Authors: Zheng, S. / Hu, H. / Ren, H. / Yang, Z. / Qiu, Q. / Qi, W. / Liu, X. / Chen, X. / Cui, X. / Li, S. / Zhou, B. / Sun, D. / Cao, X. / Du, J.
History
DepositionNov 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Transcription factor jumonji (Jmj) family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,91918
Polymers55,3351
Non-polymers1,58417
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-173 kcal/mol
Surface area22110 Å2
Unit cell
Length a, b, c (Å)129.670, 129.670, 231.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-612-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transcription factor jumonji (Jmj) family protein / JMJ13 catalytic domain


Mass: 55335.070 Da / Num. of mol.: 1 / Fragment: UNP residues 90-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: psumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: A0A1P8BAS6, UniProt: F4KIX0*PLUS

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Non-polymers , 5 types, 163 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 5.08 Å3/Da / Density % sol: 75.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES, pH 6.5, 8% dioxane, and 1.6M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.2824 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45790 / % possible obs: 100 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 36.15
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 4 / Num. unique obs: 4476 / CC1/2: 0.945 / Rpim(I) all: 0.151 / Rrim(I) all: 0.668 / Rsym value: 0.651 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→49.641 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.19
RfactorNum. reflection% reflection
Rfree0.2124 2377 5.19 %
Rwork0.1915 --
obs0.1926 45790 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 78 146 3963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073901
X-RAY DIFFRACTIONf_angle_d0.965294
X-RAY DIFFRACTIONf_dihedral_angle_d22.5011406
X-RAY DIFFRACTIONf_chiral_restr0.065566
X-RAY DIFFRACTIONf_plane_restr0.007665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3974-2.44640.30991390.26692494X-RAY DIFFRACTION100
2.4464-2.49960.28221320.24582504X-RAY DIFFRACTION100
2.4996-2.55770.24721400.21932486X-RAY DIFFRACTION100
2.5577-2.62170.28071370.21872509X-RAY DIFFRACTION100
2.6217-2.69250.24051320.20842509X-RAY DIFFRACTION100
2.6925-2.77180.27581380.21632513X-RAY DIFFRACTION100
2.7718-2.86120.2311270.21822531X-RAY DIFFRACTION100
2.8612-2.96350.21081440.21742516X-RAY DIFFRACTION100
2.9635-3.08210.29411510.22582523X-RAY DIFFRACTION100
3.0821-3.22240.21941460.21292520X-RAY DIFFRACTION100
3.2224-3.39220.27581330.20862558X-RAY DIFFRACTION100
3.3922-3.60470.20711360.1982557X-RAY DIFFRACTION100
3.6047-3.88290.22881440.19222544X-RAY DIFFRACTION100
3.8829-4.27350.1591450.16032578X-RAY DIFFRACTION100
4.2735-4.89140.16531230.14822624X-RAY DIFFRACTION100
4.8914-6.16080.18741640.18922622X-RAY DIFFRACTION100
6.1608-49.65210.19871460.18462825X-RAY DIFFRACTION100
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)
11.1705-0.8057-0.37012.58010.70771.7292-0.0746-0.15370.02510.10850.0435-0.09550.10010.11580.01960.53250.1987-0.01120.32490.01120.449841.963445.0131142.9468
21.2305-2.1505-0.9224.55471.61790.9530.0542-0.02160.2446-0.40910.0168-0.3591-0.09210.027-0.07170.63670.16680.05250.33440.04270.444753.903435.8479129.9768
34.0807-0.1332.05081.26090.65193.6172-0.1863-0.1473-0.0560.0511-0.04550.1028-0.3311-0.02160.24510.66790.16520.06040.2350.01760.498163.042812.7644130.4459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 93 through 317 )
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 484 )
3X-RAY DIFFRACTION3chain 'A' and (resid 485 through 564 )

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