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- PDB-3n9m: ceKDM7A from C.elegans, alone -

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Basic information

Entry
Database: PDB / ID: 3n9m
TitleceKDM7A from C.elegans, alone
ComponentsPutative uncharacterized protein
KeywordsOXIDOREDUCTASE / Histone / methylation / demethylase / PHD / JmjC / Fe(II) and alpha-KG (alpha-ketoglutarate)-dependent dioxygenase family
Function / homology
Function and homology information


HDMs demethylate histones / Condensation of Prophase Chromosomes / histone H3K27me2/H3K27me3 demethylase activity / 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 / histone binding / regulation of transcription by RNA polymerase II / metal 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 / JmjC domain profile. ...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 / 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
: / Lysine-specific demethylase 7 homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.493 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 1.2Mar 20, 2024Group: 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 / 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_asym_id / _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_asym_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_asym_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_asym_id / _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_asym_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
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,2648
Polymers123,8912
Non-polymers3736
Water3,963220
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1324
Polymers61,9451
Non-polymers1873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1324
Polymers61,9451
Non-polymers1873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.004, 144.515, 78.413
Angle α, β, γ (deg.)90.00, 106.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein / lysine demethylase


Mass: 61945.496 Da / Num. of mol.: 2 / 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: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18% PEG 10000, 0.1M Bis-Tris, pH 6.6, 0.2M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 29, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4928→50 Å / Num. obs: 48134 / % possible obs: 98.4 % / Biso Wilson estimate: 44.29 Å2 / Num. measured all: 269550
Reflection shellResolution: 2.4928→2.59 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.493→32.685 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7941 / SU ML: 1.98 / σ(F): 0.1 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 2314 5.07 %
Rwork0.2014 43336 -
obs0.2038 45650 93.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.653 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 132.66 Å2 / Biso mean: 55.8926 Å2 / Biso min: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.9506 Å20 Å23.5285 Å2
2--8.3356 Å2-0 Å2
3----14.2862 Å2
Refinement stepCycle: LAST / Resolution: 2.493→32.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8106 0 6 220 8332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048317
X-RAY DIFFRACTIONf_angle_d0.87111218
X-RAY DIFFRACTIONf_dihedral_angle_d17.3913081
X-RAY DIFFRACTIONf_chiral_restr0.0651154
X-RAY DIFFRACTIONf_plane_restr0.0041449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4928-2.54370.35991160.28772023X-RAY DIFFRACTION74
2.5437-2.5990.33321150.28042205X-RAY DIFFRACTION81
2.599-2.65940.34741160.26872330X-RAY DIFFRACTION85
2.6594-2.72590.35731130.25752400X-RAY DIFFRACTION87
2.7259-2.79960.28891520.24232444X-RAY DIFFRACTION90
2.7996-2.88190.26891330.23472475X-RAY DIFFRACTION90
2.8819-2.97490.26621320.23612520X-RAY DIFFRACTION93
2.9749-3.08110.31971330.25432556X-RAY DIFFRACTION94
3.0811-3.20440.3221280.24372616X-RAY DIFFRACTION96
3.2044-3.35010.26131490.23462661X-RAY DIFFRACTION97
3.3501-3.52650.24521550.2052682X-RAY DIFFRACTION98
3.5265-3.74720.23141260.18812752X-RAY DIFFRACTION99
3.7472-4.0360.19851400.1732700X-RAY DIFFRACTION99
4.036-4.44130.19391610.15112737X-RAY DIFFRACTION100
4.4413-5.08180.20121480.14982746X-RAY DIFFRACTION100
5.0818-6.39470.24141470.17912733X-RAY DIFFRACTION100
6.3947-32.68810.19151500.17742756X-RAY DIFFRACTION99

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