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- PDB-4bis: JMJD2A COMPLEXED WITH 8-HYDROXYQUINOLINE-4-CARBOXYLIC ACID -

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Basic information

Entry
Database: PDB / ID: 4bis
TitleJMJD2A COMPLEXED WITH 8-HYDROXYQUINOLINE-4-CARBOXYLIC ACID
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE / NON-HEME / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / FACIAL TRIAD / METAL BINDING PROTEIN / EPIGENETIC AND TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / HYDROXYLATION
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 / methylated histone binding / 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. / Cupin / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
8-hydroxyquinoline-4-carboxylic acid / NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsChowdhury, R. / Thinnes, C. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2013
Title: 5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation.
Authors: Hopkinson, R.J. / Tumber, A. / Yapp, C. / Chowdhury, R. / Aik, W. / Che, K.H. / Li, X.S. / Kristensen, J.B.L. / King, O.N.F. / Chan, M.C. / Yeoh, K.K. / Choi, H. / Walport, L.J. / Thinnes, C. ...Authors: Hopkinson, R.J. / Tumber, A. / Yapp, C. / Chowdhury, R. / Aik, W. / Che, K.H. / Li, X.S. / Kristensen, J.B.L. / King, O.N.F. / Chan, M.C. / Yeoh, K.K. / Choi, H. / Walport, L.J. / Thinnes, C.C. / Bush, J.T. / Lejeune, C. / Rydzik, A.M. / Rose, N.R. / Bagg, E.A. / McDonough, M.A. / Krojer, T. / Yue, W.W. / Ng, S.S. / Olsen, L. / Brennan, P.E. / Oppermann, U. / Muller-Knapp, S. / Klose, R.J. / Ratcliffe, P.J. / Schofield, C.J. / Kawamura, A.
History
DepositionApr 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)89,44211
Polymers88,6532
Non-polymers7909
Water4,738263
1
A: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7676
Polymers44,3261
Non-polymers4415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6755
Polymers44,3261
Non-polymers3494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.690, 150.150, 57.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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


Mass: 44326.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75164, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Non-polymers , 6 types, 272 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-8HQ / 8-hydroxyquinoline-4-carboxylic acid


Mass: 189.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7NO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.8 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M BIS-TRIS PROPANE PH 7.5, 0.02M NA/K PHOSPHATE, 20% W/V PEG 3350, SITTING DROP, 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2012 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.49→60.19 Å / Num. obs: 31126 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 2.49→2.56 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OX0

2ox0


Resolution: 2.493→60.187 Å / SU ML: 0.26 / σ(F): 2 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 1568 5.1 %
Rwork0.1925 --
obs0.1941 31126 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.6235 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2--1.18 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.493→60.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5592 0 40 263 5895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075816
X-RAY DIFFRACTIONf_angle_d1.267901
X-RAY DIFFRACTIONf_dihedral_angle_d15.2222085
X-RAY DIFFRACTIONf_chiral_restr0.056815
X-RAY DIFFRACTIONf_plane_restr0.0041010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4933-2.57380.31251320.27882635X-RAY DIFFRACTION100
2.5738-2.66580.30681250.26762630X-RAY DIFFRACTION100
2.6658-2.77250.26971300.2452669X-RAY DIFFRACTION100
2.7725-2.89870.2961480.24422643X-RAY DIFFRACTION99
2.8987-3.05150.29041630.24032627X-RAY DIFFRACTION100
3.0515-3.24270.22991410.21732655X-RAY DIFFRACTION100
3.2427-3.49310.25081280.20432691X-RAY DIFFRACTION100
3.4931-3.84450.23491490.19012688X-RAY DIFFRACTION100
3.8445-4.40070.18791560.15452688X-RAY DIFFRACTION100
4.4007-5.54380.16851530.14222721X-RAY DIFFRACTION100
5.5438-60.20420.19281430.17552860X-RAY DIFFRACTION99

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