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- PDB-9h44: Jumonji domain-containing protein 2B with crown ether and crystal... -

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Basic information

Entry
Database: PDB / ID: 9h44
TitleJumonji domain-containing protein 2B with crown ether and crystallization epitope mutations L916G:R917A:A918D
ComponentsLysine-specific demethylase 4B
KeywordsOXIDOREDUCTASE / crystal epitopes / Structural Genomics / Structural Genomics Consortium / SGC
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
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Lysine-specific demethylase 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Yue, W. ...Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
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. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionOct 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,0243
Polymers14,7241
Non-polymers3002
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area8280 Å2
2
A: Lysine-specific demethylase 4B
hetero molecules

A: Lysine-specific demethylase 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0486
Polymers29,4492
Non-polymers6004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_557-x+2/3,-x+y+1/3,-z+7/31
Buried area1340 Å2
ΔGint-43 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.93, 87.93, 142.91
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-957-

TYR

21A-1270-

HOH

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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
Details: Jumonji domain-containing protein 2B with crown ether and crystallization epitope mutations L916G:R917A:A918D
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-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.61 Å3/Da / Density % sol: 65.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Hampton Index well B7 0.056 M sodium phosphate monobasic 1.344 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.74→32.31 Å / Num. obs: 21921 / % possible obs: 99.3 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.5
Reflection shellResolution: 1.74→1.79 Å / Rmerge(I) obs: 0.746 / Num. unique obs: 1522

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→32.308 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.438 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.096 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2251 1107 5.05 %
Rwork0.203 20813 -
all0.204 --
obs-21920 99.257 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.007 Å20.003 Å2-0 Å2
2--0.007 Å2-0 Å2
3----0.021 Å2
Refinement stepCycle: LAST / Resolution: 1.74→32.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1010 0 19 106 1135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121131
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.8291537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.558510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02610192
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.021056
X-RAY DIFFRACTIONr_chiral_restr0.1470.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02878
X-RAY DIFFRACTIONr_nbd_refined0.2820.2459
X-RAY DIFFRACTIONr_nbtor_refined0.3180.2758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.299
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.6360.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3830.221
X-RAY DIFFRACTIONr_mcbond_it3.8693.519556
X-RAY DIFFRACTIONr_mcangle_it4.946.254709
X-RAY DIFFRACTIONr_scbond_it5.5124.163575
X-RAY DIFFRACTIONr_scangle_it7.6097.301828
X-RAY DIFFRACTIONr_lrange_it13.3542.0851745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.74-1.7850.328780.33514390.33416190.9270.9393.69980.321
1.785-1.8340.29780.29514330.29415520.9470.94497.35820.269
1.834-1.8870.284830.25114280.25315180.9530.95999.53890.218
1.887-1.9450.263640.23414060.23614730.9540.96499.79630.204
1.945-2.0080.229750.22613810.22614570.9710.96699.93140.199
2.008-2.0780.236810.22113040.22213850.9630.971000.197
2.078-2.1570.249790.20612750.20913540.9630.9741000.189
2.157-2.2440.225640.20312460.20413100.9690.9741000.186
2.244-2.3440.235690.20511580.20612280.9650.97399.91860.193
2.344-2.4570.261530.21111590.21312120.9640.9721000.203
2.457-2.5890.213520.20510840.20611360.9660.9731000.2
2.589-2.7450.253750.2079940.2110700.9610.97399.90650.211
2.745-2.9330.257410.2119750.21310160.9560.9721000.221
2.933-3.1660.273460.2099130.2129600.9620.97199.89580.228
3.166-3.4650.245360.2048280.2068640.9710.9731000.23
3.465-3.8690.188420.1997750.1998170.9790.9781000.227
3.869-4.4560.186320.1516690.1537010.9820.9861000.185
4.456-5.4320.15250.1625930.1616180.9870.9851000.209
5.432-7.5760.268250.2324600.2344850.9570.9691000.287
7.576-32.3080.13590.2172930.2143020.9890.9681000.296

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