PDB-2w2i: Crystal structure of the human 2-oxoglutarate oxygenase LOC390245

ID or keywords:

Entry

Database: PDB / ID: 2w2i

Title

Crystal structure of the human 2-oxoglutarate oxygenase LOC390245

Components

2-OXOGLUTARATE OXYGENASE

Keywords

OXIDOREDUCTASE / CHROMOSOME 11

Function / homology

Function and homology information

[histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / Zygotic genome activation (ZGA) / histone H3K9 demethylase activity / regulation of gene expression / chromatin remodeling / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Yue, W.W. / Ng, S. / Shafqat, N. / Ugochukwu, E. / McDonough, M. / Pike, A.C.W. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C. / Weigelt, J. ...

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Structural and Evolutionary Basis for the Dual Substrate Selectivity of Human Kdm4 Histone Demethylase Family.
Authors: Hillringhaus, L. / Yue, W.W. / Rose, N.R. / Ng, S.S. / Gileadi, C. / Loenarz, C. / Bello, S.H. / Bray, J.E. / Schofield, C.J. / Oppermann, U.

History

Deposition	Oct 31, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 20, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	May 13, 2015	Group: Database references / Non-polymer description ...Database references / Non-polymer description / Other / Refinement description / Source and taxonomy
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2w2i.cif.gz	209 KB	Display	PDBx/mmCIF format
PDB format	pdb2w2i.ent.gz	165.1 KB	Display	PDB format
PDBx/mmJSON format	2w2i.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w2/2w2i ftp://data.pdbj.org/pub/pdb/validation_reports/w2/2w2i	HTTPS FTP

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Related structure data

Related structure data	2xmlC 2oq7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3c0l-d 6x7n-d 6b67-2 3cer-1 7ci4-2 3tev-1 5zk4-1 2fp0-1 5oy1-d 4g4i-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2xmlC

2oq7S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (3)

Deposited unit

A: 2-OXOGLUTARATE OXYGENASE

B: 2-OXOGLUTARATE OXYGENASE

C: 2-OXOGLUTARATE OXYGENASE

hetero molecules

125 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-OXOGLUTARATE OXYGENASE

hetero molecules

defined by author&software
41.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 2-OXOGLUTARATE OXYGENASE

hetero molecules

defined by author&software
41.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 2-OXOGLUTARATE OXYGENASE

hetero molecules

defined by author&software
41.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.904, 111.009, 224.199
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 2 / Auth seq-ID: 13 - 327 / Label seq-ID: 35 - 349

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C

#1: Protein	2-OXOGLUTARATE OXYGENASE / UNCHARACTERIZED PROTEIN LOC390245 Mass: 41198.363 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-336 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: B2RXH2
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID Mass: 167.119 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₇H₅NO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.34 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99987
Detector	Type: MARRESEARCH / Detector: CCD / Date: Oct 4, 2008
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99987 Å / Relative weight: 1
Reflection	Resolution: 2.1→99 Å / Num. obs: 63031 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / R_merge(I) obs: 0.06 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2.1→2.23 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0055	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OQ7

2oq7

Resolution: 2.1→111.8 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.943 / SU B: 12.778 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.236	3333	5 %	RANDOM
R_work	0.21	-	-	-
obs	0.212	63031	99.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 14.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.29 Å²	0 Å²	0 Å²
2-	-	-0.42 Å²	0 Å²
3-	-	-	0.13 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→111.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7278	0	69	341	7688

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	7615
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	4992
X-RAY DIFFRACTION	r_angle_refined_deg	1.326	1.936	10380
X-RAY DIFFRACTION	r_angle_other_deg	0.925	3	12113
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	10.036	5	927
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.538	23.914	350
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.969	15	1095
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.065	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1075
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	8574
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1634
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.582	3	4625
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.781	5	7418
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.344	7	2990
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	6.281	11	2957
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1743	tight positional	0.04	0.05
2	B	1743	tight positional	0.04	0.05
3	C	1743	tight positional	0.04	0.05
1	A	2084	medium positional	0.07	0.5
2	B	2084	medium positional	0.05	0.5
3	C	2084	medium positional	0.06	0.5
1	A	1743	tight thermal	0.16	0.5
2	B	1743	tight thermal	0.15	0.5
3	C	1743	tight thermal	0.16	0.5
1	A	2084	medium thermal	0.13	2
2	B	2084	medium thermal	0.13	2
3	C	2084	medium thermal	0.13	2

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.388	248
R_work	0.349	4581

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.5579	-0.3129	-0.9073	3.3863	-0.1238	5.2477	-0.3078	-0.5431	-0.5953	0.5314	0.1455	0.0948	1.1577	0.3385	0.1623	0.5986	0.1405	0.0743	0.5181	0.1599	0.1358	6.668	23.162	98.548
2	2.5984	0.288	-0.3961	1.9833	0.8181	3.292	-0.1005	0.1547	0.0032	-0.1965	0.0231	-0.0552	0.0607	0.006	0.0774	0.3055	0.028	0.02	0.4228	-0.0087	0.0059	15.694	36.115	75.561
3	2.0848	-0.7514	-0.8995	0.7241	0.4035	2.1841	-0.1063	-0.0266	-0.0796	0.0277	0.1139	0.0625	0.103	-0.1922	-0.0075	0.3504	0.0104	0.0084	0.4173	0.0085	0.0314	5.12	35.45	87.62
4	1.9677	1.3396	-1.4704	2.5372	-0.1742	3.4846	0.0331	-0.5013	-0.0544	0.2919	-0.0314	0.0124	-0.0285	0.4917	-0.0017	0.339	0.086	-0.0397	0.5404	-0.0196	0.0187	16.386	38.806	92.901
5	5.3069	-3.6792	-2.8242	5.9175	2.8356	8.7074	-0.2798	-0.5255	0.1333	0.7654	0.3017	0.1265	-0.244	-0.3595	-0.0219	0.4672	0.0631	0.0344	0.617	0.0324	0.0576	-4.163	41.205	102.223
6	1.7865	-0.3192	-1.0811	2.0271	1.3864	4.7175	0.1167	-0.0658	0.0622	0.0547	-0.0394	0.1923	-0.3948	-0.1628	-0.0772	0.285	0.1005	0.0739	0.4732	-0.0015	0.0402	24.453	26.118	58.217
7	2.2834	0.5195	-1.5835	1.7564	-0.9965	4.2888	-0.3502	0.2259	-0.08	-0.3736	0.098	0.0789	0.521	-0.2529	0.2522	0.3898	0.0147	0.0267	0.4707	-0.0395	0.0596	24.798	9.153	35.158
8	0.8449	0.3881	-0.1701	0.4529	0.1843	2.3542	-0.0935	0.0343	-0.1244	-0.0039	0.1032	0.0479	0.1109	0.1111	-0.0098	0.3498	0.0816	0.0486	0.4866	0.0139	0.0697	29.497	14.243	49.265
9	0.6103	0.7013	-0.6851	3.3224	0.2197	3.5815	-0.2001	-0.1483	-0.115	0.2857	0.1095	-0.1031	0.6454	-0.0834	0.0906	0.3805	0.0826	0.1017	0.4895	0.0433	0.0773	23.927	5.122	55.343
10	2.6252	0.5555	2.2172	0.5254	0.4452	3.7163	0.0213	0.0091	-0.2584	0.1525	0.0987	-0.007	-0.0196	0.4165	-0.12	0.3321	0.0905	0.0519	0.6866	-0.0088	0.0529	40.687	15.842	60.547
11	9.2022	0.8213	2.7997	6.1164	3.9168	11.1047	-0.8006	0.9411	0.12	-1.0359	0.9695	-0.1718	-2.8599	1.0123	-0.1689	1.5449	-0.5654	0.2257	0.8041	0.0034	0.0656	59.551	30.923	90.522
12	4.0639	-0.9838	-1.1254	0.6311	-0.0985	3.3603	-0.0996	-0.1708	-0.0852	0.1513	0.0342	-0.0715	-0.2282	0.0785	0.0654	0.4736	-0.1272	0.0473	0.4484	-0.042	0.1033	64.876	14.774	112.859
13	1.2334	0.0154	0.5904	0.457	-0.1413	2.5092	0.052	0.1226	-0.065	-0.1045	0.1102	-0.1385	-0.4055	-0.1355	-0.1622	0.5905	-0.0958	0.1139	0.4992	-0.0337	0.0644	54.942	18.657	100.683
14	2.0055	-1.2007	0.5316	2.2017	-0.1562	3.5247	0.0691	0.3653	-0.293	-0.4066	0.0561	-0.0548	-0.1247	0.5414	-0.1253	0.4425	-0.152	0.1489	0.6067	-0.1077	0.1318	64.734	12.108	95.011
15	1.6829	-0.1756	2.2949	0.0536	-0.7167	10.3927	0.2935	0.1637	-0.169	0.0142	0.0766	0.024	-0.2319	-0.5121	-0.37	0.5958	0.0587	0.0442	0.7311	-0.0033	0.045	43.007	15.577	83.48

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 61
2	X-RAY DIFFRACTION	2	A	62 - 119
3	X-RAY DIFFRACTION	3	A	120 - 198
4	X-RAY DIFFRACTION	4	A	199 - 287
5	X-RAY DIFFRACTION	5	A	288 - 328
6	X-RAY DIFFRACTION	6	B	13 - 61
7	X-RAY DIFFRACTION	7	B	62 - 115
8	X-RAY DIFFRACTION	8	B	116 - 222
9	X-RAY DIFFRACTION	9	B	223 - 279
10	X-RAY DIFFRACTION	10	B	280 - 334
11	X-RAY DIFFRACTION	11	C	14 - 61
12	X-RAY DIFFRACTION	12	C	62 - 119
13	X-RAY DIFFRACTION	13	C	120 - 198
14	X-RAY DIFFRACTION	14	C	199 - 287
15	X-RAY DIFFRACTION	15	C	288 - 335

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