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- PDB-9gp4: Jumonji domain-containing protein 2A with crystallization epitope... -

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Basic information

Entry
Database: PDB / ID: 9gp4
TitleJumonji domain-containing protein 2A with crystallization epitope mutations Q953E:A958D
ComponentsLysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / Crystal Epitopes / Jumonji domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of autophagy / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol
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 ...: / : / : / 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 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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. / 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
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 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 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8098
Polymers13,3071
Non-polymers5027
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-6 kcal/mol
Surface area7560 Å2
Unit cell
Length a, b, c (Å)136.1, 136.1, 136.1
Angle α, β, γ (deg.)90, 90, 90
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

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Components

#1: Protein Lysine-specific demethylase 4A / JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A / ...JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A / [histone H3]-trimethyl-L-lysine(36) demethylase 4A / [histone H3]-trimethyl-L-lysine(9) demethylase 4A


Mass: 13306.575 Da / Num. of mol.: 1 / Mutation: Q953E, A958D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Production host: Escherichia coli (E. coli)
References: UniProt: O75164, [histone H3]-trimethyl-L-lysine9 demethylase, [histone H3]-trimethyl-L-lysine36 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.: 111 / 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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2M ammonium sulfate, 0.1M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 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: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.58→96.23 Å / Num. obs: 29690 / % possible obs: 100 % / Redundancy: 38.2 % / CC1/2: 1 / Net I/σ(I): 25.9
Reflection shellResolution: 1.58→1.62 Å / Num. unique obs: 2166 / CC1/2: 0.803

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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: 1.59→55.624 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.1 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1795 1375 4.723 %
Rwork0.161 27739 -
all0.162 --
obs-29114 99.99 %
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: 28.161 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.59→55.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 30 111 1072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121024
X-RAY DIFFRACTIONr_bond_other_d0.0020.016911
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.8311387
X-RAY DIFFRACTIONr_angle_other_deg0.8391.7622112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6565125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.38354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70110166
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.0731056
X-RAY DIFFRACTIONr_chiral_restr0.1070.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021221
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02233
X-RAY DIFFRACTIONr_nbd_refined0.1780.2119
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.2701
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2453
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2474
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.050.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.23
X-RAY DIFFRACTIONr_nbd_other0.0980.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.28
X-RAY DIFFRACTIONr_mcbond_it6.6522.356488
X-RAY DIFFRACTIONr_mcbond_other6.6072.354488
X-RAY DIFFRACTIONr_mcangle_it9.3644.253617
X-RAY DIFFRACTIONr_mcangle_other9.3754.255618
X-RAY DIFFRACTIONr_scbond_it11.8363.005536
X-RAY DIFFRACTIONr_scbond_other11.4222.938529
X-RAY DIFFRACTIONr_scangle_it16.6315.274770
X-RAY DIFFRACTIONr_scangle_other16.1725.15759
X-RAY DIFFRACTIONr_lrange_it23.3426.4971042
X-RAY DIFFRACTIONr_lrange_other22.49925.8711019
X-RAY DIFFRACTIONr_rigid_bond_restr4.86231935
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
1.59-1.6310.295890.26320280.26521170.9450.9561000.242
1.631-1.6760.264970.23419710.23620680.9580.9671000.209
1.676-1.7250.2561020.218980.20320000.960.9761000.174
1.725-1.7780.2321000.19418530.19619530.9740.9791000.161
1.778-1.8360.217860.17617990.17818850.9690.9811000.142
1.836-1.90.191820.15117630.15318450.9780.9861000.122
1.9-1.9720.22760.15516850.15817610.9740.9851000.122
1.972-2.0520.189780.14816280.1517060.980.9861000.124
2.052-2.1430.218870.14215650.14616520.9710.9881000.121
2.143-2.2480.168750.14314900.14415650.9820.9881000.122
2.248-2.3690.173710.13414340.13715050.9830.9891000.115
2.369-2.5130.172600.12913720.1314320.980.991000.109
2.513-2.6860.174590.14112790.14213390.9810.98899.92530.121
2.686-2.90.195670.15811830.15912500.9780.9851000.14
2.9-3.1760.178610.17411020.17411640.980.98199.91410.157
3.176-3.550.175500.17810110.17810610.9830.9841000.167
3.55-4.0960.139540.1568940.1559480.9890.9861000.147
4.096-5.010.135380.1267760.1268140.9870.9931000.125
5.01-7.0570.208260.1916240.1926500.9770.9871000.184
7.057-55.6240.147170.2133840.214010.9860.9751000.206

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