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- PDB-9t2h: Jumonji domain-containing protein 2B with crystallization epitope... -

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Basic information

Entry
Database: PDB / ID: 9t2h
TitleJumonji domain-containing protein 2B with crystallization epitope mutations L916G:R917A:A918D
ComponentsLysine-specific demethylase 4B
KeywordsOXIDOREDUCTASE / Crystal epitopes
Function / homology
Function and homology information


histone H3K36 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / HDMs demethylate histones / brain development / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / Estrogen-dependent gene expression ...histone H3K36 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / HDMs demethylate histones / brain development / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / Estrogen-dependent gene expression / chromatin remodeling / chromatin / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. ...: / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Lysine-specific demethylase 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. ...Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants
Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. ...Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionOct 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine-specific demethylase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2278
Polymers14,7241
Non-polymers5027
Water66737
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)91.04, 91.04, 102.26
Angle α, β, γ (deg.)90, 90, 120
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Lysine-specific demethylase 4B / JmjC domain-containing histone demethylation protein 3B / Jumonji domain-containing protein 2B / ...JmjC domain-containing histone demethylation protein 3B / Jumonji domain-containing protein 2B / [histone H3]-trimethyl-L-lysine(9) demethylase 4B


Mass: 14724.405 Da / Num. of mol.: 1 / Mutation: L916G:R917A:A918D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4B, JHDM3B, JMJD2B, KIAA0876 / Production host: Escherichia coli (E. coli)
References: UniProt: O94953, [histone H3]-trimethyl-L-lysine9 demethylase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.15 Å3/Da / Density % sol: 70.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.15M DL- malic acid 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.96→62.47 Å / Num. obs: 18610 / % possible obs: 100 % / Redundancy: 18.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.3
Reflection shellResolution: 1.96→2.01 Å / Rmerge(I) obs: 2.319 / Num. unique obs: 1348

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→62.44 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.136
RfactorNum. reflection% reflectionSelection details
Rfree0.2795 831 -RANDOM
Rwork0.2686 ---
obs0.2692 17759 100 %-
Displacement parametersBiso mean: 47.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.9842 Å20 Å20 Å2
2--2.9842 Å20 Å2
3----5.9683 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 1.99→62.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 30 38 1071
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081043HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.881402HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d364SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes175HARMONIC5
X-RAY DIFFRACTIONt_it1043HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion131SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact691SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion14.25
LS refinement shellResolution: 1.99→2.01 Å
RfactorNum. reflection% reflection
Rfree0.341 14 -
Rwork0.3416 --
obs0.3416 434 99.76 %

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