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- PDB-3dxu: The crystal structure of core JMJD2D complexed with FE and N-oxal... -

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Basic information

Entry
Database: PDB / ID: 3dxu
TitleThe crystal structure of core JMJD2D complexed with FE and N-oxalylglycine
ComponentsJmjC domain-containing histone demethylation protein 3D
KeywordsOXIDOREDUCTASE / JMJD2D / JMJC / NOG / Histone demethylase / 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 / 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 / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / 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 / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus
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
: / N-OXALYLGLYCINE / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, Z. / Zhang, G.
CitationJournal: To be Published
Title: The Crystal Structure of Core Jmjd2D
Authors: Chen, Z. / Zhang, G.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 4, 2018Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_distant_solvent_atoms ...database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.3Dec 11, 2019Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _database_PDB_caveat.text / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._database_PDB_caveat.text / _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_ref_seq_dif.details
Revision 1.4Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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_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: JmjC domain-containing histone demethylation protein 3D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,53210
Polymers38,6991
Non-polymers8339
Water6,575365
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)79,06320
Polymers77,3972
Non-polymers1,66618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6090 Å2
ΔGint-137.9 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.543, 71.543, 150.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-708-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 38698.707 Da / Num. of mol.: 1 / Fragment: UNP residues 8-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD2D, JHDM3D / Plasmid: PGEXT 4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta DE3
References: UniProt: Q6B0I6, 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, 374 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, pH6.50, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 22344 / Num. obs: 20644

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.95 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.128 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1045 5.1 %RANDOM
Rwork0.168 ---
obs0.17 19398 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.142 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 45 365 3102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222807
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.9433781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7635330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17523.688141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85815454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0591517
X-RAY DIFFRACTIONr_chiral_restr0.1280.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022175
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21385
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21864
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5040.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0721.51708
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60722643
X-RAY DIFFRACTIONr_scbond_it2.78931295
X-RAY DIFFRACTIONr_scangle_it4.0614.51138
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 79 -
Rwork0.193 1322 -
obs--94.85 %
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)
12.9702-0.3549-0.92492.71190.89823.06280.0314-0.0033-0.310.0834-0.0140.24210.3032-0.4354-0.0175-0.1053-0.0749-0.0392-0.11590.0716-0.1148-6.0952-6.724321.3208
21.2769-0.17660.22473.31913.5876.95290.04110.02510.1595-0.37770.1159-0.2906-0.53140.2796-0.1569-0.1430.00310.0026-0.12240.0423-0.1423.11287.277916.8536
32.1849-0.32970.70750.6960.06960.89430.0703-0.044-0.1743-0.02050.0006-0.03270.1522-0.0077-0.071-0.0692-0.00440.007-0.14760.0334-0.160911.6451-1.499115.8858
41.37420.09260.41950.84030.12961.31760.0504-0.06640.07680.0549-0.0345-0.0229-0.0399-0.007-0.0159-0.1517-0.0204-0.0068-0.14970.0323-0.1958.08115.639423.1501
54.39071.8663.02336.244-0.66542.7796-0.09540.215-0.0205-0.0335-0.106-0.5703-0.28130.66670.2015-0.10150.02160.0297-0.01990.0084-0.0905-0.033519.587111.631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 604 - 53
2X-RAY DIFFRACTION2AA71 - 9864 - 91
3X-RAY DIFFRACTION3AA99 - 17592 - 168
4X-RAY DIFFRACTION4AA176 - 297169 - 290
5X-RAY DIFFRACTION5AA298 - 340291 - 333

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