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- PDB-3dxt: Crystal structure of the catalytic core domain of JMJD2D -

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Basic information

Entry
Database: PDB / ID: 3dxt
TitleCrystal structure of the catalytic core domain of JMJD2D
ComponentsJmjC domain-containing histone demethylation protein 3D
KeywordsOXIDOREDUCTASE / NUCLEAR PROTEIN / JMJD2D / JMJC / histone demethylase / H3K9 / JUMONJI domain-containing protein 2D / Chromatin regulator / Dioxygenase / Iron / Metal-binding / Nucleus / Transcription / Transcription regulation
Function / homology
Function and homology information


: / : / positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone methyltransferase complex / dioxygenase activity / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity ...: / : / positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone methyltransferase complex / dioxygenase activity / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / regulation of protein phosphorylation / double-strand break repair via homologous recombination / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / damaged DNA binding / blood microparticle / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lysine-specific demethylase 4D / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, Z. / Zhang, G.
CitationJournal: To be Published
Title: Crystal structure of the catalytic core domain of jmjd2d
Authors: Chen, Z. / Zhang, G.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: JmjC domain-containing histone demethylation protein 3D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5189
Polymers40,7961
Non-polymers7228
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: JmjC domain-containing histone demethylation protein 3D
hetero molecules

A: JmjC domain-containing histone demethylation protein 3D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,03718
Polymers81,5932
Non-polymers1,44416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5650 Å2
ΔGint-107.5 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.630, 71.630, 151.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein JmjC domain-containing histone demethylation protein 3D / Jumonji domain-containing protein 2D


Mass: 40796.301 Da / Num. of mol.: 1 / Fragment: Catalytic core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: jmjd2d / Plasmid: PGEXT-4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3)
References: UniProt: Q0VF39, UniProt: Q6B0I6*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation ...References: UniProt: Q0VF39, UniProt: Q6B0I6*PLUS, 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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: hepes, 2.0M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorDate: Feb 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 36000 / Num. obs: 34305

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: jmjd2a

Resolution: 1.8→41.24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.993 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 1693 4.9 %RANDOM
Rwork0.17407 ---
obs0.17554 32633 91.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.515 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 40 291 3026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222791
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9423769
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47823.643140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64715452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0271517
X-RAY DIFFRACTIONr_chiral_restr0.0990.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022158
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21338
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21897
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2210
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3931.51701
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97822640
X-RAY DIFFRACTIONr_scbond_it3.5131275
X-RAY DIFFRACTIONr_scangle_it4.8844.51129
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 127 -
Rwork0.224 2500 -
obs--97.77 %
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)
12.0242-0.4587-1.14551.42650.50163.95360.0344-0.0073-0.21250.0079-0.06730.17640.3295-0.39570.0329-0.0574-0.0727-0.0185-0.07080.0355-0.0562-5.756-6.92921.439
20.58030.02560.1582.91033.3317.40270.03720.1040.069-0.21620.0488-0.1276-0.26370.2821-0.086-0.0916-0.0055-0.0109-0.03060.0342-0.052623.3547.28616.837
31.5267-0.2780.27280.81610.02391.1120.10530.0423-0.1488-0.0089-0.0586-0.04410.09420.0663-0.0468-0.02860.0096-0.0025-0.09620.0043-0.08911.823-1.5215.825
40.90580.02170.31410.825-0.06231.05740.0302-0.01780.03610.059-0.0427-0.0003-0.02280.07130.0125-0.0967-0.0161-0.0066-0.0990.0189-0.11018.3075.5223.255
55.28352.26571.79725.4777-1.23011.5607-0.08580.43140.1488-0.0885-0.1261-0.3381-0.09290.49440.212-0.04080.01680.01650.06170.0379-0.04020.34219.25411.672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 6011 - 60
2X-RAY DIFFRACTION2AA71 - 9871 - 98
3X-RAY DIFFRACTION3AA99 - 17599 - 175
4X-RAY DIFFRACTION4AA176 - 297176 - 297
5X-RAY DIFFRACTION5AA298 - 340298 - 340

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