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- PDB-3n9l: ceKDM7A from C.elegans, complex with H3K4me3 peptide and NOG -

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Basic information

Entry
Database: PDB / ID: 3n9l
TitleceKDM7A from C.elegans, complex with H3K4me3 peptide and NOG
Components
  • Histone H3 peptide
  • Putative uncharacterized protein
KeywordsOXIDOREDUCTASE / histone / methylation / demethylase / PHD / Jmjc / Fe(II) and alpha-KG (alpha-ketoglutarate)-dependent dioxygenase family
Function / homology
Function and homology information


PKMTs methylate histone lysines / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / HDMs demethylate histones / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / : / : / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape ...PKMTs methylate histone lysines / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / HDMs demethylate histones / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / : / : / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / : / Condensation of Prophase Chromosomes / histone H3K27me2/H3K27me3 demethylase activity / mitochondrial unfolded protein response / 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 / histone H3K9 demethylase activity / histone demethylase activity / transcription coregulator activity / structural constituent of chromatin / nucleosome / histone binding / chromatin remodeling / protein heterodimerization activity / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / : / Zinc/RING finger domain, C3HC4 (zinc finger) / Cupin / Herpes Virus-1 / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1360 / Jumonji, helical domain / Jumonji helical domain / : / Zinc/RING finger domain, C3HC4 (zinc finger) / Cupin / Herpes Virus-1 / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Histone H3 / Lysine-specific demethylase 7 homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.796 Å
AuthorsYang, Y. / Hu, L. / Wang, P. / Hou, H. / Chen, C.D. / Xu, Y.
CitationJournal: Cell Res. / Year: 2010
Title: Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans
Authors: Yang, Y. / Hu, L. / Wang, P. / Hou, H. / Lin, Y. / Liu, Y. / Li, Z. / Gong, R. / Feng, X. / Zhou, L. / Zhang, W. / Dong, Y. / Yang, H. / Lin, H. / Wang, Y. / Chen, C.D. / Xu, Y.
History
DepositionMay 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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: Putative uncharacterized protein
B: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8876
Polymers63,5532
Non-polymers3344
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-3 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.912, 87.264, 102.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Putative uncharacterized protein / lysine demethylase


Mass: 61945.496 Da / Num. of mol.: 1 / Fragment: PHD domain, UNP residues 201-724
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F29B9.2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9GYI0, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Protein/peptide Histone H3 peptide


Mass: 1607.877 Da / Num. of mol.: 1 / Fragment: JMJC domain, UNP residues 2-16 / Source method: obtained synthetically / Details: chemical synthesis, purchased from a company / Source: (synth.) Caenorhabditis elegans (invertebrata) / References: UniProt: P08898

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Non-polymers , 4 types, 100 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG 3350, 0.2M Sodium Fluoride, 0.1M Bis-Tris/HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2828 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 6, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828 Å / Relative weight: 1
ReflectionResolution: 2.796→50 Å / Num. obs: 15846 / % possible obs: 100 % / Biso Wilson estimate: 41.98 Å2 / Num. measured all: 128353
Reflection shellResolution: 2.796→2.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N9M

3n9m


Resolution: 2.796→44.189 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.825 / SU ML: 0.31 / σ(F): 0.15 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 768 5.01 %
Rwork0.197 14557 -
obs0.1999 15325 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.832 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 124.14 Å2 / Biso mean: 44.9357 Å2 / Biso min: 14.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.8274 Å20 Å2-0 Å2
2--3.6362 Å20 Å2
3----4.4637 Å2
Refinement stepCycle: LAST / Resolution: 2.796→44.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 13 96 4158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044161
X-RAY DIFFRACTIONf_angle_d0.8325617
X-RAY DIFFRACTIONf_dihedral_angle_d14.6781569
X-RAY DIFFRACTIONf_chiral_restr0.055579
X-RAY DIFFRACTIONf_plane_restr0.003726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7961-3.01190.30621340.23742732X-RAY DIFFRACTION91
3.0119-3.31490.3041490.22982788X-RAY DIFFRACTION95
3.3149-3.79440.27741640.19682946X-RAY DIFFRACTION98
3.7944-4.77960.23321510.16462961X-RAY DIFFRACTION99
4.7796-44.19480.20911700.18443130X-RAY DIFFRACTION99

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