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- PDB-6a58: Structure of histone demethylase REF6 -

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Basic information

Entry
Database: PDB / ID: 6a58
TitleStructure of histone demethylase REF6
ComponentsLysine-specific demethylase REF6
KeywordsDNA BINDING PROTEIN / Complex / histone demethylase REF6 / DNA / zinc finger
Function / homology
Function and homology information


regulation of ethylene-activated signaling pathway / abscisic acid catabolic process / release of seed from dormancy / positive regulation of lateral root development / : / response to diterpene / : / heat acclimation / protein localization to heterochromatin / : ...regulation of ethylene-activated signaling pathway / abscisic acid catabolic process / release of seed from dormancy / positive regulation of lateral root development / : / response to diterpene / : / heat acclimation / protein localization to heterochromatin / : / response to brassinosteroid / sugar mediated signaling pathway / unidimensional cell growth / regulation of photoperiodism, flowering / systemic acquired resistance / vegetative to reproductive phase transition of meristem / : / ethylene-activated signaling pathway / histone H3K27me2/H3K27me3 demethylase activity / leaf development / 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 / response to abscisic acid / Ino80 complex / abscisic acid-activated signaling pathway / epigenetic regulation of gene expression / response to mechanical stimulus / protein homooligomerization / : / response to heat / sequence-specific DNA binding / regulation of DNA-templated transcription / positive regulation of gene expression / metal ion binding / nucleus
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / zinc finger / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger C2H2 type domain profile. ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / zinc finger / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Lysine-specific demethylase REF6
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.57 Å
AuthorsTian, Z. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2016YFC1200400 China
CitationJournal: Cell Discov / Year: 2020
Title: Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms.
Authors: Tian, Z. / Li, X. / Li, M. / Wu, W. / Zhang, M. / Tang, C. / Li, Z. / Liu, Y. / Chen, Z. / Yang, M. / Ma, L. / Caba, C. / Tong, Y. / Lam, H.M. / Dai, S. / Chen, Z.
History
DepositionJun 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Mar 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: Lysine-specific demethylase REF6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7835
Polymers16,5221
Non-polymers2624
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.494, 62.494, 43.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Lysine-specific demethylase REF6 / Jumonji domain-containing protein 12 / Lysine-specific histone demethylase REF6 / Protein RELATIVE ...Jumonji domain-containing protein 12 / Lysine-specific histone demethylase REF6 / Protein RELATIVE OF EARLY FLOWERING 6


Mass: 16521.723 Da / Num. of mol.: 1 / Fragment: Ig gamma-1 chain C region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: REF6, JMJ12, PKDM9A, At3g48430, T29H11_50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STM3, 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 23425 / % possible obs: 99.7 % / Redundancy: 12.8 % / Rsym value: 0.057 / Net I/σ(I): 76.8
Reflection shellResolution: 1.57→1.6 Å / Num. unique obs: 1174 / Rsym value: 0.496 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: MAD / Resolution: 1.57→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.614 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23384 1187 5.1 %RANDOM
Rwork0.21085 ---
obs0.21199 22150 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.563 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 4 119 1052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019980
X-RAY DIFFRACTIONr_bond_other_d0.0010.02857
X-RAY DIFFRACTIONr_angle_refined_deg0.9671.8981320
X-RAY DIFFRACTIONr_angle_other_deg0.81631990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7875119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.18121.48947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07915168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.217159
X-RAY DIFFRACTIONr_chiral_restr0.0540.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1293.576467
X-RAY DIFFRACTIONr_mcbond_other1.1273.568466
X-RAY DIFFRACTIONr_mcangle_it1.9985.351583
X-RAY DIFFRACTIONr_mcangle_other1.9975.359584
X-RAY DIFFRACTIONr_scbond_it1.1663.679513
X-RAY DIFFRACTIONr_scbond_other1.1663.679513
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9165.47736
X-RAY DIFFRACTIONr_long_range_B_refined4.18641.1381121
X-RAY DIFFRACTIONr_long_range_B_other3.86640.5481102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.571→1.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 70 -
Rwork0.297 1656 -
obs--99.31 %

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