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

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Basic information

Entry
Database: PDB / ID: 9gle
TitleJumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S
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 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 ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / 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 / methylated histone binding / 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
NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 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
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,84217
Polymers83,7412
Non-polymers1,10115
Water8,035446
1
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,59311
Polymers41,8711
Non-polymers72310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2496
Polymers41,8711
Non-polymers3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.7, 90.78, 90.67
Angle α, β, γ (deg.)90, 107.19, 90
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 9 - 354 / Label seq-ID: 9 - 354

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#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: 41870.617 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 461 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulfate, 25% PEG3350, 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: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.88→40.449 Å / Num. obs: 73694 / % possible obs: 99.5 % / Redundancy: 3.4 % / CC1/2: 0.997 / Net I/σ(I): 12.5
Reflection shellResolution: 1.88→1.93 Å / Num. unique obs: 5432 / CC1/2: 0.783

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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: 1.88→40.449 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.638 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2223 3667 4.976 %
Rwork0.1854 70026 -
all0.187 --
obs-73693 99.447 %
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: 39.163 Å2
Baniso -1Baniso -2Baniso -3
1-1.908 Å20 Å20.588 Å2
2--1.152 Å20 Å2
3----2.873 Å2
Refinement stepCycle: LAST / Resolution: 1.88→40.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 53 446 5997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125805
X-RAY DIFFRACTIONr_bond_other_d0.0030.0165167
X-RAY DIFFRACTIONr_angle_refined_deg2.0531.8247895
X-RAY DIFFRACTIONr_angle_other_deg0.8631.74411935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.906532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59410901
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.51710273
X-RAY DIFFRACTIONr_chiral_restr0.1140.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026889
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021427
X-RAY DIFFRACTIONr_nbd_refined0.2080.21102
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.24738
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22868
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2395
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2690.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5840.231
X-RAY DIFFRACTIONr_nbd_other0.1830.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.6850.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.230.24
X-RAY DIFFRACTIONr_mcbond_it4.8433.752790
X-RAY DIFFRACTIONr_mcbond_other4.8443.752790
X-RAY DIFFRACTIONr_mcangle_it6.16.7173498
X-RAY DIFFRACTIONr_mcangle_other6.16.7183499
X-RAY DIFFRACTIONr_scbond_it5.4034.0323015
X-RAY DIFFRACTIONr_scbond_other5.4024.0323016
X-RAY DIFFRACTIONr_scangle_it7.3797.2354397
X-RAY DIFFRACTIONr_scangle_other7.3787.2354398
X-RAY DIFFRACTIONr_lrange_it8.85838.3616685
X-RAY DIFFRACTIONr_lrange_other8.85938.3316574
X-RAY DIFFRACTIONr_ncsr_local_group_10.1010.0511112
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.101050.05008
12BX-RAY DIFFRACTIONLocal ncs0.101050.05008
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
1.88-1.9290.3192590.28951560.2954650.9280.93699.08510.268
1.929-1.9810.3152620.25650390.25853200.9320.95299.64290.231
1.981-2.0390.2742390.2448580.24251330.950.95899.29870.216
2.039-2.1010.2522430.22247970.22350610.9540.96599.58510.198
2.101-2.170.2612190.20545830.20848260.9560.97199.50270.183
2.17-2.2460.2662250.244760.20347300.950.97399.38690.18
2.246-2.330.2372190.18743100.18945410.9650.97699.73570.169
2.33-2.4250.2552310.19741110.243580.9590.97499.63290.182
2.425-2.5330.2392160.1939660.19241970.9570.97799.64260.177
2.533-2.6560.2532200.18538240.18940530.9590.97899.77790.177
2.656-2.7990.2282050.17935720.18137960.9650.98199.49950.173
2.799-2.9680.2061930.17834210.17936240.9720.9899.72410.176
2.968-3.1710.2131820.18931810.1933840.9710.97999.37940.192
3.171-3.4240.2411900.20529840.20731900.9660.97699.49840.215
3.424-3.7480.2461230.1927910.19229330.9610.97999.35220.202
3.748-4.1860.1961150.1624930.16226420.9790.98498.71310.182
4.186-4.8250.1631220.13322170.13423550.9820.9999.32060.158
4.825-5.8880.145880.15818990.15719990.9880.98899.39970.188
5.888-8.240.185710.17614910.17615750.9780.98399.17460.202
8.24-40.4490.225450.1958570.1969110.9670.97499.01210.227

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