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

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Basic information

Entry
Database: PDB / ID: 9gii
TitleJumonji domain-containing protein 2A with crystallization epitope mutation R913A
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 / apoptotic chromosome condensation / 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 / negative regulation of astrocyte differentiation ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / 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 / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / 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 / positive regulation of gene expression / 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: 1.7 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
DepositionAug 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 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 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6425
Polymers13,2621
Non-polymers3804
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-29 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.87, 133.87, 133.87
Angle α, β, γ (deg.)90, 90, 90
Int Tables number214
Space group name H-MI4132

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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: 13261.580 Da / Num. of mol.: 1 / Mutation: R913A
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.77 Å3/Da / Density % sol: 67.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2M ammonium sulfate, 0.1M bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→47.375 Å / Num. obs: 22799 / % possible obs: 100 % / Redundancy: 39.1 % / CC1/2: 0.994 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.74 Å / Num. unique obs: 1650 / CC1/2: 0.962

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.375 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.721 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.081 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2158 1108 4.864 %
Rwork0.198 21672 -
all0.199 --
obs-22780 99.982 %
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: 28.102 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 21 88 1033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.012962
X-RAY DIFFRACTIONr_angle_refined_deg2.4591.8051307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.76853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25410150
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.5821052
X-RAY DIFFRACTIONr_chiral_restr0.1740.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02749
X-RAY DIFFRACTIONr_nbd_refined0.2050.2367
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.290
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0690.216
X-RAY DIFFRACTIONr_mcbond_it3.3642.24463
X-RAY DIFFRACTIONr_mcangle_it4.6163.983577
X-RAY DIFFRACTIONr_scbond_it5.3092.97499
X-RAY DIFFRACTIONr_scangle_it7.6535.166730
X-RAY DIFFRACTIONr_lrange_it11.1232.6141462
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
1.7-1.7450.241640.26215850.26116490.9650.9571000.225
1.745-1.7920.283870.26115280.26216150.9470.9591000.224
1.792-1.8440.274760.24714900.24815670.9560.9699.93620.218
1.844-1.9010.241670.21714560.21815230.9590.9691000.193
1.901-1.9630.239800.21913890.2214690.9640.9691000.199
1.963-2.0320.238730.21213690.21314420.9650.9711000.196
2.032-2.1080.244640.20813250.2113890.9550.9721000.199
2.108-2.1940.265610.21512760.21713370.9550.971000.209
2.194-2.2920.257720.20612010.20912730.9510.9721000.202
2.292-2.4030.203730.20111570.20112300.9750.9741000.2
2.403-2.5330.234550.20111180.20311730.970.9741000.204
2.533-2.6860.25670.21710530.21911200.960.9691000.226
2.686-2.8710.195460.1989980.19810440.9740.9731000.211
2.871-3.10.15490.1879380.1859870.9820.9781000.208
3.1-3.3940.178380.1718730.1729120.9820.98299.89040.198
3.394-3.7930.225270.1728090.1748360.9760.9831000.206
3.793-4.3750.179320.1627020.1627340.9850.9851000.2
4.375-5.3460.145350.1616080.166430.990.9851000.207
5.346-7.5130.315260.2474900.255160.9690.971000.303
7.513-47.3750.244160.2363070.2363230.960.9631000.331

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