PDB-4liu: Structure of YcfD, a Ribosomal oxygenase from Escherichia coli.

ID or keywords:

Entry

Database: PDB / ID: 4liu

Title

Structure of YcfD, a Ribosomal oxygenase from Escherichia coli.

Components

50S ribosomal protein L16 arginine hydroxylase

Keywords

OXIDOREDUCTASE / JmjC Domain / Dioxygenase / Hydroxylation

Function / homology

Function and homology information

[50S ribosomal protein L16]-arginine 3-hydroxylase / histone H3K36 demethylase activity / histone H3K4 demethylase activity / 2-oxoglutarate-dependent dioxygenase activity / post-translational protein modification / ferrous iron binding / protein homodimerization activity
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.7 Å

Authors

Brissett, N.C. / Doherty, A.J. / Fox, G.C.

Citation

Journal: Nature / Year: 2014
Title: Ribosomal oxygenases are structurally conserved from prokaryotes to humans.
Authors: Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R. / Vollmar, M. / Phillips, C. / Pilka, E.S. ...

History

Deposition	Jul 3, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 25, 2014	Group: Database references
Revision 1.2	Jul 9, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4liu.cif.gz	160.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4liu.ent.gz	131.9 KB	Display	PDB format
PDBx/mmJSON format	4liu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4liu_validation.pdf.gz	451.5 KB	Display	wwPDB validaton report
Full document	4liu_full_validation.pdf.gz	453.9 KB	Display
Data in XML	4liu_validation.xml.gz	15.9 KB	Display
Data in CIF	4liu_validation.cif.gz	21.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/li/4liu ftp://data.pdbj.org/pub/pdb/validation_reports/li/4liu	HTTPS FTP

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Related structure data

Related structure data	2xdvC 4bu2C 4bxfC 4ccjC 4cckC 4cclC 4ccmC 4ccnC 4ccoC 4cswC 4cugC 4litC 4livC C: citing same article (ref.)
Similar structure data	4nub-1 4liv-1 4lit-1 4ccl-d 2qkd-d 3tz4-2 5yzd-d 1y5x-d 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

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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: 50S ribosomal protein L16 arginine hydroxylase

hetero molecules

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

1

A: 50S ribosomal protein L16 arginine hydroxylase

hetero molecules

A: 50S ribosomal protein L16 arginine hydroxylase

hetero molecules

defined by author&software
94.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.110, 75.110, 209.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	50S ribosomal protein L16 arginine hydroxylase / Ribosomal oxygenase YcfD / ROX Mass: 46834.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1128, JW1114, ycfD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834s References: UniProt: P27431, 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
#2: Chemical	ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₇NO₃ / Comment: pH buffer*YM
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.17 Å³/Da / Density % sol: 61.17 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM Tris.HCl pH 7.5, 0.4M Ammonium dihydrogen phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: BM16 / Wavelength: 0.9798 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2006 / Details: double crystal monochromator

Radiation

Monochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9798 Å / Relative weight: 1

Reflection

Redundancy: 6.1 % / Av σ(I) over netI: 5.2 / Number: 106655 / R_sym value: 0.142 / D res high: 2.7 Å / D res low: 70.721 Å / Num. obs: 17365 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
8.54	43.02	98.4	1	0.029	0.029	4.9
6.04	8.54	99.6	1	0.05	0.05	5.7
4.93	6.04	99.8	1	0.058	0.058	5.9
4.27	4.93	99.9	1	0.056	0.056	6.1
3.82	4.27	99.8	1	0.085	0.085	6.2
3.49	3.82	99.9	1	0.148	0.148	6.2
3.23	3.49	100	1	0.218	0.218	6.3
3.02	3.23	100	1	0.381	0.381	6.3
2.85	3.02	100	1	0.601	0.601	6.3
2.7	2.85	100	1	0.872	0.872	6.3

Reflection

Resolution: 2.7→70.721 Å / Num. all: 17365 / Num. obs: 17365 / % possible obs: 99.9 % / Redundancy: 6.1 % / R_sym value: 0.142 / Net I/σ(I): 11

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
2.7-2.85	6.3	0.872	0.9	0.872	1	100
2.85-3.02	6.3	0.601	1.3	0.601	1	100
3.02-3.23	6.3	0.381	2	0.381	1	100
3.23-3.49	6.3	0.218	3.5	0.218	1	100
3.49-3.82	6.2	0.148	4.9	0.148	1	99.9
3.82-4.27	6.2	0.085	8.9	0.085	1	99.8
4.27-4.93	6.1	0.056	13	0.056	1	99.9
4.93-6.04	5.9	0.058	12.6	0.058	1	99.8
6.04-8.54	5.7	0.05	14.7	0.05	1	99.6
8.54-43.024	4.9	0.029	19	0.029	1	98.4

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2.7 Å / D res low: 42.31 Å / FOM acentric: 0.233 / FOM centric: 0.057 / Reflection acentric: 14190 / Reflection centric: 3099

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	2.7	42.31	14190	3099
ANO_1	0.894	0	2.7	42.31	14190	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	Reflection acentric	Reflection centric
ISO_1	11.63-42.31	0	120	143
ISO_1	8.39-11.63	0	249	148
ISO_1	6.89-8.39	0	345	155
ISO_1	5.99-6.89	0	418	151
ISO_1	5.37-5.99	0	482	151
ISO_1	4.91-5.37	0	548	159
ISO_1	4.55-4.91	0	594	155
ISO_1	4.26-4.55	0	643	158
ISO_1	4.01-4.26	0	691	156
ISO_1	3.81-4.01	0	732	145
ISO_1	3.63-3.81	0	777	165
ISO_1	3.48-3.63	0	819	157
ISO_1	3.35-3.48	0	854	154
ISO_1	3.22-3.35	0	874	160
ISO_1	3.12-3.22	0	923	154
ISO_1	3.02-3.12	0	959	154
ISO_1	2.93-3.02	0	1005	164
ISO_1	2.85-2.93	0	1020	154
ISO_1	2.77-2.85	0	1045	162
ISO_1	2.7-2.77	0	1092	154
ANO_1	11.63-42.31	0.336	120	0
ANO_1	8.39-11.63	0.32	249	0
ANO_1	6.89-8.39	0.398	345	0
ANO_1	5.99-6.89	0.47	418	0
ANO_1	5.37-5.99	0.629	482	0
ANO_1	4.91-5.37	0.631	548	0
ANO_1	4.55-4.91	0.71	594	0
ANO_1	4.26-4.55	0.789	643	0
ANO_1	4.01-4.26	0.835	691	0
ANO_1	3.81-4.01	0.892	732	0
ANO_1	3.63-3.81	0.906	777	0
ANO_1	3.48-3.63	0.949	819	0
ANO_1	3.35-3.48	0.959	854	0
ANO_1	3.22-3.35	0.968	874	0
ANO_1	3.12-3.22	0.981	923	0
ANO_1	3.02-3.12	0.993	959	0
ANO_1	2.93-3.02	0.993	1005	0
ANO_1	2.85-2.93	0.998	1020	0
ANO_1	2.77-2.85	1.001	1045	0
ANO_1	2.7-2.77	1.007	1092	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-61.238	-39.547	-17.06	SE	52.54	0.25
2	-55.873	-47.422	-29.466	SE	66.91	0.24
3	-38.127	-43.394	-48.366	SE	63.18	0.23
4	-57.022	-24.055	-1.988	SE	69.97	0.22
5	-73.244	-68.912	-11.569	SE	51.12	0.18
6	-5.46	-61.238	-5.699	SE	82.77	0.24
7	-71.434	-30.03	-23.417	SE	95.82	0.18
8	-53.116	-36.736	-24.849	SE	110.94	0.15
9	-14.146	-74.363	-25.349	SE	75.59	0.08

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
11.63-42.31	0.623	0.079	120	143
8.39-11.63	0.597	0.092	249	148
6.89-8.39	0.573	0.094	345	155
5.99-6.89	0.522	0.084	418	151
5.37-5.99	0.458	0.094	482	151
4.91-5.37	0.462	0.065	548	159
4.55-4.91	0.419	0.054	594	155
4.26-4.55	0.37	0.05	643	158
4.01-4.26	0.344	0.047	691	156
3.81-4.01	0.286	0.04	732	145
3.63-3.81	0.26	0.04	777	165
3.48-3.63	0.211	0.047	819	157
3.35-3.48	0.195	0.042	854	154
3.22-3.35	0.154	0.041	874	160
3.12-3.22	0.135	0.043	923	154
3.02-3.12	0.112	0.045	959	154
2.93-3.02	0.102	0.051	1005	164
2.85-2.93	0.09	0.042	1020	154
2.77-2.85	0.078	0.053	1045	162
2.7-2.77	0.068	0.041	1092	154

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.21	data scaling
SHARP		phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2.7→43.024 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.37 / σ(F): 1.01 / Phase error: 23.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2373	1590	5.07 %
R_work	0.1966	-	-
obs	0.1986	31369	99.5 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 40.9965 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→43.024 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2875	0	16	113	3004

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2989
X-RAY DIFFRACTION	f_angle_d	0.807	4074
X-RAY DIFFRACTION	f_dihedral_angle_d	15.2	1099
X-RAY DIFFRACTION	f_chiral_restr	0.06	417
X-RAY DIFFRACTION	f_plane_restr	0.003	545

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 (%)
2.7-2.7872	0.3857	162	0.2948	2690	X-RAY DIFFRACTION	99
2.7872-2.8868	0.3245	163	0.2753	2709	X-RAY DIFFRACTION	100
2.8868-3.0023	0.2944	140	0.27	2693	X-RAY DIFFRACTION	100
3.0023-3.1389	0.3033	174	0.2622	2711	X-RAY DIFFRACTION	100
3.1389-3.3043	0.2408	131	0.2173	2717	X-RAY DIFFRACTION	100
3.3043-3.5113	0.2194	142	0.1921	2696	X-RAY DIFFRACTION	100
3.5113-3.7822	0.2267	147	0.1898	2737	X-RAY DIFFRACTION	100
3.7822-4.1626	0.2246	136	0.1581	2710	X-RAY DIFFRACTION	100
4.1626-4.7643	0.168	154	0.1475	2692	X-RAY DIFFRACTION	100
4.7643-5.9999	0.2261	100	0.1732	2749	X-RAY DIFFRACTION	99
5.9999-43.0289	0.2329	141	0.1983	2675	X-RAY DIFFRACTION	98

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	8.4649	4.8263	-2.9061	6.4569	3.4402	8.0058	0.5197	-0.0361	-1.5878	0.4629	0.4337	-1.5751	0.695	1.3202	-0.3373	0.422	0.2808	-0.0227	0.6123	-0.0357	0.5195	22.2184	-18.418	31.1742
2	2.0525	1.654	-0.0359	1.8297	0.371	3.6234	-0.1184	-0.104	-0.5186	-0.0773	0.1213	-0.1254	0.4798	-0.3276	-0.0097	0.2137	-0.0176	0.0318	0.2149	-0.0121	0.2479	6.878	-16.1279	32.7988
3	3.9507	-0.3216	-1.5133	4.3546	0.7294	5.8428	0.2987	-0.0161	0.5722	-0.7135	0.2688	-0.4286	-1.204	0.2107	-0.3747	0.4289	-0.1473	-0.0006	0.4068	-0.0056	0.3214	22.8528	6.7613	30.4907
4	2.7482	-0.8239	-0.2051	1.0759	1.2178	3.393	0.1544	0.1338	-0.0031	-0.219	0.322	-0.7118	-0.4395	0.5838	-0.2975	0.295	-0.0639	0.0458	0.3331	-0.0288	0.2832	21.2648	-2.7954	27.3533
5	2.6185	0.2839	0.2857	3.0854	0.8033	3.8299	0.2355	-0.1202	0.2226	0.0909	-0.1036	0.1016	-0.4809	0.0003	-0.0758	0.2371	0.0148	0.0193	0.2115	0.0028	0.2064	9.7747	-2.3931	34.2245
6	2.5272	-1.9131	2.599	1.6971	-1.2706	4.0146	0.1498	-0.1044	0.1086	-0.0623	-0.0203	-0.0209	0.3718	0.1514	-0.146	0.3184	0.0395	0.0362	0.2505	0.0552	0.2587	-5.9257	0.429	-7.0225
7	6.6771	-2.266	3.4256	2.4221	-1.9138	2.0928	0.4664	1.0505	-0.2876	-0.6465	-0.2064	-0.1092	0.723	0.7256	-0.1914	0.5192	0.239	0.0292	0.5855	0.1007	0.3153	8.3666	-8.1959	3.071
8	3.0369	-2.1228	-0.6645	2.4343	-0.308	3.041	0.2498	0.2143	0.2593	-0.2313	-0.1207	-0.1689	-0.1978	-0.1323	-0.1569	0.205	0.0539	0.0445	0.2785	0.0069	0.2416	27.5488	-14.2774	7.4129
9	2.9065	-1.1196	-0.9207	4.4259	0.1359	2.0396	0.0248	0.0006	-0.2149	-0.0378	-0.1122	0.2876	0.1875	-0.0155	0.0912	0.2019	0.0405	0.0176	0.324	-0.0186	0.2335	27.1664	-20.6002	6.3548

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 35:39)
2	X-RAY DIFFRACTION	2	(chain A and resid 40:66)
3	X-RAY DIFFRACTION	3	(chain A and resid 67:99)
4	X-RAY DIFFRACTION	4	(chain A and resid 100:140)
5	X-RAY DIFFRACTION	5	(chain A and resid 141:237)
6	X-RAY DIFFRACTION	6	(chain A and resid 238:290)
7	X-RAY DIFFRACTION	7	(chain A and resid 291:310)
8	X-RAY DIFFRACTION	8	(chain A and resid 311:360)
9	X-RAY DIFFRACTION	9	(chain A and resid 361:407)

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