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- PDB-4ask: CRYSTAL STRUCTURE OF JMJD3 WITH GSK-J1 -

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Entry
Database: PDB / ID: 4ask
TitleCRYSTAL STRUCTURE OF JMJD3 WITH GSK-J1
ComponentsLYSINE-SPECIFIC DEMETHYLASE 6B
KeywordsOXIDOREDUCTASE / KDM6B / GSK-J1 / INHIBITOR / LYSINE SPECIFIC HISTONE DEMETHYLASE
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / histone demethylase activity / cell fate commitment / response to fungicide ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / histone demethylase activity / cell fate commitment / response to fungicide / Chromatin modifications during the maternal to zygotic transition (MZT) / response to activity / hippocampus development / HDMs demethylate histones / chromatin DNA binding / beta-catenin binding / cellular response to hydrogen peroxide / positive regulation of cold-induced thermogenesis / regulation of gene expression / Oxidative Stress Induced Senescence / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Cupin / JmjC domain, hydroxylase ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribbon / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Chem-K0I / Lysine-specific demethylase 6B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsChung, C. / Mosley, J. / Liddle, J.
CitationJournal: Nature / Year: 2012
Title: A Selective Jumonji H3K27 Demethylase Inhibitor Modulates the Proinflammatory Macrophage Response
Authors: Kruidenier, L. / Chung, C. / Cheng, Z. / Liddle, J. / Che, K. / Joberty, G. / Bantscheff, M. / Bountra, C. / Bridges, A. / Diallo, H. / Eberhard, D. / Hutchinson, S. / Jones, E. / Katso, R. ...Authors: Kruidenier, L. / Chung, C. / Cheng, Z. / Liddle, J. / Che, K. / Joberty, G. / Bantscheff, M. / Bountra, C. / Bridges, A. / Diallo, H. / Eberhard, D. / Hutchinson, S. / Jones, E. / Katso, R. / Leveridge, M. / Mander, P.K. / Mosley, J. / Ramirez-Molina, C. / Rowland, P. / Schofield, C.J. / Sheppard, R.J. / Smith, J.E. / Swales, C. / Tanner, R. / Thomas, P. / Tumber, A. / Drewes, G. / Oppermann, U. / Patel, D.J. / Lee, K. / Wilson, D.M.
History
DepositionMay 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Dec 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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

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Assembly

Deposited unit
A: LYSINE-SPECIFIC DEMETHYLASE 6B
B: LYSINE-SPECIFIC DEMETHYLASE 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1288
Polymers116,1012
Non-polymers1,0286
Water22,3211239
1
A: LYSINE-SPECIFIC DEMETHYLASE 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5644
Polymers58,0501
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5644
Polymers58,0501
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.359, 65.554, 77.392
Angle α, β, γ (deg.)85.98, 67.69, 68.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 6B / JMJC DOMAIN-CONTAINING PROTEIN 3 / JUMONJI DOMAIN-CONTAINING PROTEIN 3 / LYSINE DEMETHYLASE 6B JMJD3


Mass: 58050.285 Da / Num. of mol.: 2 / Fragment: CATALYTIC AND ZBD DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: O15054, 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K0I / 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid / 3-((6-(4,5-dihydro-1H-benzo[d]azepin-3(2H)-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid


Mass: 389.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N5O2
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1239 / 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: 2.3 Å3/Da / Density % sol: 46.5 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS HCL, BICINE PH 8.5, 37.5% MPD, PEG1K, PEG3350, 0.03M MGCL2, 0.03M CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.86→40 Å / Num. obs: 83457 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XUE

2xue


Resolution: 1.86→71.37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.442 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20882 3319 4 %RANDOM
Rwork0.16471 ---
obs0.16646 80137 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.283 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-1.41 Å2-0.1 Å2
2--1.33 Å21.22 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.86→71.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6800 0 62 1239 8101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.027184
X-RAY DIFFRACTIONr_bond_other_d0.0010.024803
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9339819
X-RAY DIFFRACTIONr_angle_other_deg0.797311685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10223.812341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.909151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3591546
X-RAY DIFFRACTIONr_chiral_restr0.0620.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021535
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 225 -
Rwork0.237 5684 -
obs--91.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6161-0.17740.2870.1835-0.1930.5307-0.003-0.00180.01950.00320.00190.0025-0.0202-0.0190.00110.0497-0.0064-0.00460.008-0.0110.025157.380217.1219-13.8749
20.5998-0.14660.23160.5133-0.20520.4765-0.01530.0428-0.0488-0.00790.0278-0.0480.0117-0.0477-0.01250.0382-0.00030.01720.0179-0.01290.037874.670646.250319.4864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1141 - 1643
2X-RAY DIFFRACTION2B1141 - 1643

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