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- PDB-3pur: CEKDM7A from C.Elegans, complex with D-2-HG -

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Basic information

Entry
Database: PDB / ID: 3pur
TitleCEKDM7A from C.Elegans, complex with D-2-HG
ComponentsLysine-specific demethylase 7 homolog
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / demethylase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / nucleus / metal ion binding
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 / 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
(2R)-2-hydroxypentanedioic acid / : / Lysine-specific demethylase 7 homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYang, Y. / Wang, P. / Xu, W. / Xu, Y.
CitationJournal: Cancer Cell / Year: 2011
Title: Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases
Authors: Xu, W. / Yang, H. / Liu, Y. / Yang, Y. / Wang, P. / Kim, S.-H. / Ito, S. / Yang, C. / Wang, P. / Xiao, M.-T. / Liu, L.-X. / Jiang, W.-Q. / Liu, J. / Zhang, J.-Y. / Wang, B. / Frye, S. / ...Authors: Xu, W. / Yang, H. / Liu, Y. / Yang, Y. / Wang, P. / Kim, S.-H. / Ito, S. / Yang, C. / Wang, P. / Xiao, M.-T. / Liu, L.-X. / Jiang, W.-Q. / Liu, J. / Zhang, J.-Y. / Wang, B. / Frye, S. / Zhang, Y. / Xu, Y.-H. / Lei, Q.-Y. / Guan, K.-L. / Zhao, S.-M. / Xiong, Y.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Mar 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: Lysine-specific demethylase 7 homolog
C: Lysine-specific demethylase 7 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,56110
Polymers123,8912
Non-polymers6708
Water5,350297
1
A: Lysine-specific demethylase 7 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2805
Polymers61,9451
Non-polymers3354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Lysine-specific demethylase 7 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2805
Polymers61,9451
Non-polymers3354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.009, 144.086, 78.087
Angle α, β, γ (deg.)90.00, 106.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysine-specific demethylase 7 homolog / LYSINE DEMETHYLASE / ceKDM7A / PHD finger protein 8 homolog / PHF8 homolog


Mass: 61945.496 Da / Num. of mol.: 2 / Fragment: PHD domain
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: Chemical ChemComp-2HG / (2R)-2-hydroxypentanedioic acid


Mass: 148.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18% PEG 10000, 0.1M BIS-TRIS, 0.2M SODIUM FORMATE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 70867 / % possible obs: 96.4 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / SU ML: 0.28 / σ(F): 0.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 3545 5 %
Rwork0.214 --
obs0.2158 70867 87.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.115 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.645 Å2-0 Å25.0229 Å2
2--5.1828 Å20 Å2
3----21.8278 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8062 0 26 297 8385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088306
X-RAY DIFFRACTIONf_angle_d1.11711200
X-RAY DIFFRACTIONf_dihedral_angle_d16.7363128
X-RAY DIFFRACTIONf_chiral_restr0.0881153
X-RAY DIFFRACTIONf_plane_restr0.0051442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12930.3415970.24821654X-RAY DIFFRACTION53
2.1293-2.15970.28491070.26631961X-RAY DIFFRACTION65
2.1597-2.19190.35531040.27172075X-RAY DIFFRACTION67
2.1919-2.22620.34751170.25832199X-RAY DIFFRACTION71
2.2262-2.26270.3091130.24532339X-RAY DIFFRACTION75
2.2627-2.30170.31131250.24352502X-RAY DIFFRACTION81
2.3017-2.34350.28591270.25142472X-RAY DIFFRACTION80
2.3435-2.38860.29831390.24772568X-RAY DIFFRACTION84
2.3886-2.43740.29611400.24742640X-RAY DIFFRACTION84
2.4374-2.49030.33021440.2412658X-RAY DIFFRACTION87
2.4903-2.54830.32871320.24842727X-RAY DIFFRACTION87
2.5483-2.6120.27671500.24912701X-RAY DIFFRACTION88
2.612-2.68260.2921620.24972776X-RAY DIFFRACTION90
2.6826-2.76150.38031380.25332874X-RAY DIFFRACTION92
2.7615-2.85060.28241440.25222856X-RAY DIFFRACTION93
2.8506-2.95250.27891610.24712931X-RAY DIFFRACTION95
2.9525-3.07070.28041450.25832955X-RAY DIFFRACTION96
3.0707-3.21040.26591500.24932996X-RAY DIFFRACTION96
3.2104-3.37950.29281680.23683014X-RAY DIFFRACTION97
3.3795-3.59110.23621580.21483036X-RAY DIFFRACTION98
3.5911-3.86820.24791530.19793091X-RAY DIFFRACTION99
3.8682-4.25710.20481690.17253044X-RAY DIFFRACTION99
4.2571-4.87220.18211780.15913082X-RAY DIFFRACTION99
4.8722-6.13510.20021670.17333109X-RAY DIFFRACTION100
6.1351-500.22131570.18423062X-RAY DIFFRACTION97

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