PDB-6f4o: Human JMJD5 in complex with Mn(II) and Succinate.

ID or keywords:

Entry

Database: PDB / ID: 6f4o

Title

Human JMJD5 in complex with Mn(II) and Succinate.

Components

JmjC domain-containing protein 5

Keywords

OXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / JMJC / JMJC DOMAIN / Lysine-specific demethylase 8 / JmjC domain-containing protein 5 / Arginyl C-3 Hydroxylase / JMJD5 / KDM8 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSLATION / DSBH / FACIAL TRIAD / CYTOPLASM / JMJC HYDROXYLASE / JMJC DEMETHYLASE / KDMS / POST-TRANSLATIONAL MODIFICATIONS / PTM / BETA-HYDROXYLATION / HYDROXYLATION / ARGININE HYDROXYLATION / RCC1 domain-containing protein 1 / RCCD1 / Regulator of chromosome condensation / 40S ribosomal protein S6 / RPS6 / RIBOSOME BIOGENESIS / TRANSCRIPTION / EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / TRANSCRIPTION ACTIVATOR/INHIBITOR / PHOSPHORYLATION / CANCER / POLYMORPHISM

Function / homology

Function and homology information

[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.28 Å

Authors

Chowdhury, R. / Islam, M.S. / Schofield, C.J.

Citation

Journal: Nat Commun / Year: 2018
Title: JMJD5 is a human arginyl C-3 hydroxylase.
Authors: Wilkins, S.E. / Islam, S. / Gannon, J.M. / Markolovic, S. / Hopkinson, R.J. / Ge, W. / Schofield, C.J. / Chowdhury, R.

History

Deposition	Nov 29, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 4, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: 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 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6f4o.cif.gz	173.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6f4o.ent.gz	138.8 KB	Display	PDB format
PDBx/mmJSON format	6f4o.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6f4o_validation.pdf.gz	453.6 KB	Display	wwPDB validaton report
Full document	6f4o_full_validation.pdf.gz	454 KB	Display
Data in XML	6f4o_validation.xml.gz	14.8 KB	Display
Data in CIF	6f4o_validation.cif.gz	22.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f4/6f4o ftp://data.pdbj.org/pub/pdb/validation_reports/f4/6f4o	HTTPS FTP

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Related structure data

Related structure data	6f4mC 6f4nC 6f4pC 6f4qC 6f4rC 6f4sC 6f4tC 4gjzS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6f4r-1 6f4q-d 6f4t-d 6zb6-2 4gaz-2 6f4p-d 4qu1-d 5n9m-1 6f4r-d 6i9l-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (5)

Deposited unit

A: JmjC domain-containing protein 5

hetero molecules

29.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	49.434, 64.411, 77.491
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	JmjC domain-containing protein 5 / JmjC domain-containing protein 5 / Jumonji domain-containing protein 5 Mass: 29602.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CATALYTIC DOMAIN (RESIDUES 183-416) / Source: (gene. exp.) Homo sapiens (human) / Gene: KDM8, JMJD5 / Plasmid: PNIC28 BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8N371, [50S ribosomal protein L16]-arginine 3-hydroxylase
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₄
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.33 Å³/Da / Density % sol: 47.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 2:1 ratio)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2017 / Details: MIRRORS
Radiation	Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.28→27.56 Å / Num. obs: 64327 / % possible obs: 99.7 % / Redundancy: 7.1 % / B_iso Wilson estimate: 16 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.081 / R_pim(I) all: 0.035 / Net I/σ(I): 19.5
Reflection shell	Resolution: 1.28→1.33 Å / Redundancy: 7.4 % / R_merge(I) obs: 1.1 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6378 / CC_1/2: 0.663 / R_pim(I) all: 0.491 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-2000	706E	data reduction
HKL-2000	706E	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4GJZ

4gjz

Resolution: 1.28→27.56 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.27 / Stereochemistry target values: ML
Details: REFINEMENT TARGET : ML and BULK SOLVENT MODELLING METHOD USED : FLAT MODEL

	R_factor	Num. reflection	% reflection
R_free	0.1744	3259	5.07 %
R_work	0.1457	-	-
obs	0.147	64244	99.67 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / B_sol: 51.6 Å² / k_sol: 0.4 e/Å³

Displacement parameters

B_iso mean: 26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.87 Å²	0 Å²	0 Å²
2-	-	-1.23 Å²	0 Å²
3-	-	-	5.09 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.18 Å	0.17 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	-	0.2 Å

Refinement step

Cycle: LAST / Resolution: 1.28→27.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1864	0	17	303	2184

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2219
X-RAY DIFFRACTION	f_angle_d	1.121	3057
X-RAY DIFFRACTION	f_dihedral_angle_d	14.064	831
X-RAY DIFFRACTION	f_chiral_restr	0.086	313
X-RAY DIFFRACTION	f_plane_restr	0.009	413

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.28-1.2991	0.2711	149	0.2645	2599	X-RAY DIFFRACTION	99
1.2991-1.3194	0.2583	145	0.2541	2620	X-RAY DIFFRACTION	100
1.3194-1.341	0.2732	141	0.2459	2633	X-RAY DIFFRACTION	100
1.341-1.3642	0.2103	137	0.2332	2618	X-RAY DIFFRACTION	100
1.3642-1.389	0.2502	145	0.2217	2613	X-RAY DIFFRACTION	100
1.389-1.4157	0.2614	150	0.2117	2621	X-RAY DIFFRACTION	100
1.4157-1.4446	0.2135	149	0.1946	2629	X-RAY DIFFRACTION	100
1.4446-1.476	0.2035	134	0.1746	2638	X-RAY DIFFRACTION	100
1.476-1.5103	0.1868	142	0.163	2637	X-RAY DIFFRACTION	100
1.5103-1.5481	0.1697	140	0.1524	2639	X-RAY DIFFRACTION	100
1.5481-1.5899	0.1871	154	0.1505	2618	X-RAY DIFFRACTION	100
1.5899-1.6367	0.1616	141	0.1434	2631	X-RAY DIFFRACTION	100
1.6367-1.6895	0.1773	146	0.139	2637	X-RAY DIFFRACTION	100
1.6895-1.7499	0.1457	152	0.1371	2651	X-RAY DIFFRACTION	100
1.7499-1.82	0.1577	136	0.1274	2646	X-RAY DIFFRACTION	100
1.82-1.9028	0.1631	135	0.1268	2696	X-RAY DIFFRACTION	100
1.9028-2.0031	0.1275	161	0.1186	2618	X-RAY DIFFRACTION	100
2.0031-2.1285	0.1376	122	0.1203	2675	X-RAY DIFFRACTION	100
2.1285-2.2928	0.1504	147	0.1261	2688	X-RAY DIFFRACTION	100
2.2928-2.5234	0.1537	124	0.135	2682	X-RAY DIFFRACTION	100
2.5234-2.8882	0.1742	143	0.1404	2712	X-RAY DIFFRACTION	99
2.8882-3.6375	0.1645	132	0.1368	2704	X-RAY DIFFRACTION	99
3.6375-27.5683	0.1988	134	0.1512	2780	X-RAY DIFFRACTION	97

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	1.1649	-0.5677	-0.0613	0.7728	0.1594	1.5104	0.0468	0.0401	0.2308	0.0601	0.13	0.2046	-0.3182	-0.3771	0.0698	0.169	0.0534	0.0418	0.2118	0.0424	0.215	-24.256	22.9473	-20.3272
2	0.1706	0.1827	-0.0415	0.2737	-0.2077	0.5538	-0.1649	-0.1994	0.1111	0.2454	0.2326	-0.1071	-0.1408	-0.0421	-0.0001	0.2608	0.0396	0.0096	0.2592	-0.0212	0.151	-8.2888	10.8291	-2.8306
3	0.6779	-0.5181	0.229	0.8188	0.1928	0.2609	0.1037	0.1585	-0.0887	-0.1965	-0.0789	-0.1154	0.0867	0.1354	-0.0002	0.2224	0.0297	0.0351	0.1881	0.0124	0.1768	2.5328	1.7276	-17.0819
4	0.5937	-0.904	0.0912	1.1387	-0.6127	1.2441	0.038	0.2037	0.1225	0.0789	-0.1463	-0.2374	0.0046	0.3156	-0.0011	0.1527	-0.0066	0.0006	0.1963	0.0317	0.2151	5.5469	8.1526	-13.9042
5	0.5021	-0.2219	-0.1462	0.5406	-0.549	0.2128	-0.1129	-0.0719	-0.3136	0.0622	0.1355	0.2535	0.1416	-0.2269	0.0056	0.2117	-0.0167	0.0294	0.2216	0.0631	0.3027	-19.4401	4.8632	-12.4668
6	0.0721	-0.009	-0.0009	0.0676	-0.1505	0.131	-0.0837	-0.047	0.14	-0.0886	0.0698	0.1639	-0.0006	0.0422	-0	0.1454	0.0007	-0.0102	0.1276	-0.0059	0.1835	-8.4416	7.9174	-16.2482
7	0.0626	0.0089	-0.1276	0.0912	-0.3097	0.676	0.0772	0.0371	-0.0938	0.0222	-0.0128	-0.0402	0.0917	0.0671	-0.0002	0.1416	0.0004	-0.0156	0.1338	-0.0174	0.1481	-7.2306	13.3289	-26.1072
8	0.2548	-0.2248	-0.1849	0.1751	-0.2206	0.3827	0.0093	-0.037	0.0143	0.077	0.0492	0.0281	-0.0883	0.0144	-0	0.1473	0.0031	0.0042	0.1231	-0.0003	0.1321	-10.3244	18.7903	-19.8255
9	0.8149	-0.0226	-0.8328	0.3516	-0.539	1.2868	-0.0449	0.3156	-0.3847	-0.1931	-0.0071	-0.0281	0.0996	-0.0346	0	0.2022	-0.0126	0.0152	0.1978	-0.0473	0.2075	-8.0116	14.0911	-37.2945
10	0.2338	0.1563	-0.2619	0.4599	-0.0117	0.2086	0.2062	0.1304	0.1376	-0.0634	-0.0145	-0.1283	-0.2739	0.0586	0.006	0.2116	0.0204	0.0605	0.2151	0.0079	0.1627	-2.0198	24.582	-39.1507
11	0.4949	0.0354	-0.3809	0.231	-0.4549	0.4387	0.008	0.0148	0.0526	0.0541	0.055	0.0726	-0.1347	-0.0581	0	0.1451	0.01	0.0084	0.1389	-0.0088	0.1395	-14.482	19.551	-22.6624
12	0.2463	-0.2046	-0.3935	0.6067	-0.4155	0.9551	-0.0082	0.0363	-0.0731	0.0549	0.0395	0.0046	-0.0135	-0.0434	-0	0.1378	-0.0036	-0.0075	0.1277	-0.0056	0.1432	-10.6225	13.3781	-19.2494

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 182:211)
2	X-RAY DIFFRACTION	2	(chain A and resid 212:230)
3	X-RAY DIFFRACTION	3	(chain A and resid 231:254)
4	X-RAY DIFFRACTION	4	(chain A and resid 255:277)
5	X-RAY DIFFRACTION	5	(chain A and resid 278:305)
6	X-RAY DIFFRACTION	6	(chain A and resid 306:312)
7	X-RAY DIFFRACTION	7	(chain A and resid 313:325)
8	X-RAY DIFFRACTION	8	(chain A and resid 326:341)
9	X-RAY DIFFRACTION	9	(chain A and resid 342:365)
10	X-RAY DIFFRACTION	10	(chain A and resid 366:381)
11	X-RAY DIFFRACTION	11	(chain A and resid 382:399)
12	X-RAY DIFFRACTION	12	(chain A and resid 400:416)

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