PDB-6qo7: Crystal structure of ribonucleotide reductase NrdF from Bacillus ...

ID or keywords:

Entry

Database: PDB / ID: 6qo7

Title

Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis aerobically soaked with ferrous ions (photo-reduced)

Components

Ribonucleoside-diphosphate reductase subunit beta

Keywords

OXIDOREDUCTASE / Metal binding / Oxidation reduction process / 2'-Deoxyribonucleotide metabolism / DNA replication

Function / homology

Function and homology information

ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane / metal ion binding
Similarity search - Function

Biological species

Bacillus anthracis str. Sterne (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.628 Å

Authors

Grave, K. / Hogbom, M.

Citation

Journal: J.Biol.Inorg.Chem. / Year: 2019
Title: Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access.
Authors: Grave, K. / Lambert, W. / Berggren, G. / Griese, J.J. / Bennett, M.D. / Logan, D.T. / Hogbom, M.

History

Deposition	Feb 12, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 21, 2019	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Oct 2, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	May 15, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6qo7.cif.gz	351.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6qo7.ent.gz	294.2 KB	Display	PDB format
PDBx/mmJSON format	6qo7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6qo7_validation.pdf.gz	429.6 KB	Display	wwPDB validaton report
Full document	6qo7_full_validation.pdf.gz	431 KB	Display
Data in XML	6qo7_validation.xml.gz	24.2 KB	Display
Data in CIF	6qo7_validation.cif.gz	35.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qo/6qo7 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/6qo7	HTTPS FTP

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Related structure data

Related structure data	6qo5C 6qo8C 6qo9C 6qobC C: citing same article (ref.)
Similar structure data	6qo5-d 4bmr-d 6qo8-d 6tqw-d 6tqv-d 3gye-d 3w76-d 4bmt-d 4ef9-d 6ebo-2 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	#238 - Oct 2019 Ribonucleotide Reductase similarity (7) #111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

Deposited unit

A: Ribonucleoside-diphosphate reductase subunit beta

B: Ribonucleoside-diphosphate reductase subunit beta

hetero molecules

74.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	57.293, 59.958, 95.360
Angle α, β, γ (deg.)	90.00, 107.11, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ribonucleoside-diphosphate reductase subunit beta Mass: 37055.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis str. Sterne (bacteria) Gene: nrdF, GBAA_1372 / Variant: pXO1-/pXO2- deficient / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 References: UniProt: Q81TB4, ribonucleoside-diphosphate reductase
#2: Chemical	ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.11 Å³/Da / Density % sol: 41.77 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 - 2.0 M ammonium sulphate, 0.1 M Bis-Tris methane, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 1.628→41.819 Å / Num. obs: 77191 / % possible obs: 99.61 % / Redundancy: 3.8 % / B_iso Wilson estimate: 19.44 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.062 / R_pim(I) all: 0.036 / R_rim(I) all: 0.072 / Net I/σ(I): 12.8
Reflection shell	Resolution: 1.628→1.69 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.628 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 7581 / CC_1/2: 0.778 / R_pim(I) all: 0.366 / R_rim(I) all: 0.729 / % possible all: 98.35

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Processing

Software

Name	Version	Classification
SCALA		data scaling
XDS		data reduction
PHASER		phasing
PHENIX	(1.12_2829: ???)	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.628→41.819 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.7

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1916	3860	5 %	Random selection
R_work	0.1589	-	-	-
obs	0.1605	77191	99.62 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 25.36 Å²

Refinement step

Cycle: LAST / Resolution: 1.628→41.819 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4698	0	5	317	5020

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	4850
X-RAY DIFFRACTION	f_angle_d	1.185	6567
X-RAY DIFFRACTION	f_dihedral_angle_d	19.262	1792
X-RAY DIFFRACTION	f_chiral_restr	0.063	730
X-RAY DIFFRACTION	f_plane_restr	0.008	838

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 (%)
1.6281-1.6479	0.3414	129	0.2921	2464	X-RAY DIFFRACTION	96
1.6479-1.6688	0.2685	139	0.2798	2625	X-RAY DIFFRACTION	100
1.6688-1.6907	0.3004	136	0.2581	2588	X-RAY DIFFRACTION	100
1.6907-1.7139	0.2779	138	0.2495	2620	X-RAY DIFFRACTION	100
1.7139-1.7384	0.2558	138	0.2353	2627	X-RAY DIFFRACTION	100
1.7384-1.7643	0.2275	138	0.2277	2627	X-RAY DIFFRACTION	100
1.7643-1.7919	0.2433	137	0.2154	2590	X-RAY DIFFRACTION	100
1.7919-1.8213	0.2516	138	0.214	2622	X-RAY DIFFRACTION	100
1.8213-1.8527	0.2163	136	0.1968	2598	X-RAY DIFFRACTION	100
1.8527-1.8864	0.2124	138	0.1866	2614	X-RAY DIFFRACTION	100
1.8864-1.9227	0.2125	138	0.1918	2620	X-RAY DIFFRACTION	100
1.9227-1.9619	0.1984	137	0.1785	2600	X-RAY DIFFRACTION	100
1.9619-2.0046	0.1981	137	0.1653	2616	X-RAY DIFFRACTION	100
2.0046-2.0512	0.1835	140	0.1655	2655	X-RAY DIFFRACTION	100
2.0512-2.1025	0.1698	135	0.1571	2572	X-RAY DIFFRACTION	100
2.1025-2.1593	0.2124	139	0.1473	2640	X-RAY DIFFRACTION	100
2.1593-2.2229	0.1701	140	0.1431	2645	X-RAY DIFFRACTION	100
2.2229-2.2946	0.1978	137	0.1412	2613	X-RAY DIFFRACTION	100
2.2946-2.3766	0.167	137	0.1355	2601	X-RAY DIFFRACTION	100
2.3766-2.4718	0.1574	138	0.1387	2627	X-RAY DIFFRACTION	100
2.4718-2.5843	0.1869	139	0.1459	2642	X-RAY DIFFRACTION	100
2.5843-2.7205	0.2057	139	0.1475	2628	X-RAY DIFFRACTION	100
2.7205-2.8909	0.2055	139	0.1575	2651	X-RAY DIFFRACTION	100
2.8909-3.114	0.1952	137	0.1542	2593	X-RAY DIFFRACTION	100
3.114-3.4273	0.1843	139	0.145	2656	X-RAY DIFFRACTION	100
3.4273-3.9229	0.1513	140	0.1212	2653	X-RAY DIFFRACTION	100
3.9229-4.9412	0.1532	140	0.1192	2663	X-RAY DIFFRACTION	100
4.9412-10	0.2071	142	0.1843	2681	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	3.2032	-0.1308	-1.9833	1.4837	-1.2253	4.0806	0.2728	-0.5174	-0.1723	0.2659	-0.2827	-0.4827	-0.0932	0.7616	-0.0006	0.2046	0.01	-0.0712	0.337	-0.0102	0.2432	75.752	-0.2051	37.2486
2	0.5157	-0.4756	0.5962	0.579	-0.8148	5.5044	-0.0252	0.0645	0.1699	-0.0475	-0.0212	-0.0483	-0.5771	-0.303	0.0494	0.234	0.0026	-0.0011	0.181	0.0105	0.2197	68.6154	12.8512	10.9005
3	1.0885	0.0764	-0.6218	3.1314	-3.4757	6.5026	0.0756	0.1952	0.0651	-0.4159	-0.0692	0.0914	0.2371	-0.0684	0.0079	0.1851	0.0298	-0.0211	0.1904	0.0113	0.1688	67.5685	1.2131	0.1509
4	1.0611	-0.2689	0.2535	1.2516	-0.437	1.9785	0.0552	0.141	-0.0017	-0.1665	0.0067	0.0381	0.048	-0.0574	-0.0843	0.1415	-0.0017	-0.0048	0.1924	-0.0019	0.1626	65.0165	-0.1395	11.3792
5	1.9793	-0.4994	0.6673	2.1059	-1.8973	2.2086	0.0995	0.2036	-0.2132	-0.2847	-0.1012	0.0007	0.6321	-0.2448	0.0199	0.1757	-0.0002	-0.0033	0.1481	-0.03	0.1874	71.5593	-13.6649	9.1677
6	2.9186	0.5269	-0.252	1.8734	-0.4276	1.6843	-0.0196	-0.2349	-0.1752	0.08	0.0284	0.0252	0.0786	0.066	-0.0059	0.1286	0.0265	0.0108	0.1435	0.0081	0.1731	77.1552	-12.5544	19.6125
7	0.9828	-0.6311	0.2903	1.6096	-0.9518	2.1698	-0.0061	0.0585	0.1063	-0.0717	0.0139	-0.0511	-0.1876	-0.0085	-0.0188	0.1319	-0.0149	0.0182	0.1312	0.004	0.1469	77.6641	3.8826	10.4146
8	2.5274	-1.9803	2.6944	3.1294	-3.151	6.2348	0.1324	0.0745	-0.1625	-0.2819	-0.0228	-0.0244	0.1596	0.1301	-0.1286	0.1743	0.0152	0.0412	0.1501	-0.0152	0.1748	82.4701	-10.9809	4.6393
9	2.1288	-1.282	1.7792	2.3883	-2.6847	7.7337	0.1391	0.285	0.1958	-0.2516	-0.2496	-0.2095	-0.0847	0.4259	0.0945	0.1658	0.0093	0.0428	0.1759	0.0248	0.1839	85.4321	0.1276	2.9072
10	1.0415	-2.2479	1.6888	4.8942	-3.715	2.8437	-0.0883	0.1359	0.2559	0.3323	-0.0936	-0.2049	-0.3638	0.3327	0.1875	0.2284	-0.052	0.0301	0.2111	0.0516	0.2802	86.593	6.7578	6.103
11	2.601	0.3333	-1.7183	1.7015	0.6206	3.5887	0.1565	0.4886	-0.2558	-0.2075	-0.1317	0.1735	-0.0235	-0.5412	-0.0396	0.177	0.0065	-0.0575	0.3205	-0.0045	0.2138	53.9058	-1.0791	7.943
12	0.5068	0.4129	0.749	0.577	1.7624	6.9645	-0.0551	-0.0455	0.1236	-0.0858	0.0496	0.0629	-0.5738	0.299	0.0309	0.2164	0.002	-0.0186	0.1765	-0.0183	0.2183	60.0068	12.9336	34.2127
13	1.3227	-0.4682	-0.5742	3.0911	3.0674	5.6059	0.0115	-0.1972	0.0929	0.4454	0.1538	-0.1398	0.3316	0.1698	-0.1435	0.1914	0.0075	-0.0146	0.1664	-0.0214	0.1564	61.8922	1.7543	45.2349
14	4.274	-1.9481	0.0923	4.8313	-2.0792	1.2428	0.0722	-0.0171	-0.251	-0.124	0.0834	0.2522	0.219	-0.0929	-0.1748	0.1296	-0.0245	-0.0255	0.1642	-0.0036	0.1917	59.3108	-9.2477	20.9792
15	1.5016	0.5468	1.7671	1.4007	1.6203	5.7166	-0.0269	-0.0507	0.0931	0.0341	0.0544	0.0069	0.0077	0.1068	-0.0313	0.1202	0.0012	0.0033	0.168	-0.0126	0.1605	63.0156	4.4054	30.4962
16	3.2744	2.7076	0.3907	8.2999	1.469	3.3371	0.2009	-0.4157	-0.0674	0.8597	-0.1938	-0.589	0.3882	0.4123	0.0187	0.3289	0.0585	-0.0934	0.3455	-0.0227	0.2184	70.5372	-0.3131	48.912
17	1.1899	0.5244	0.5863	2.359	2.4201	2.4848	0.0809	-0.176	-0.1765	0.3147	-0.045	-0.074	0.5875	0.1963	-0.0552	0.1945	0.0062	-0.0055	0.1719	0.0113	0.1836	58.8673	-13.769	36.8792
18	3.5085	-0.6793	-0.386	2.5103	0.5411	1.4846	0.0483	0.1615	-0.1615	-0.0466	-0.048	0.027	0.0724	-0.0343	-0.0005	0.1178	-0.0158	0.0059	0.1379	-0.0034	0.1468	53.4438	-13.36	26.3278
19	1.1285	0.8252	0.7184	2.1247	0.9867	1.6284	-0.086	-0.0678	0.108	0.0678	0.0111	0.1688	-0.0534	0.0112	0.0735	0.1061	0.0133	0.0136	0.123	-0.0146	0.1494	51.6212	3.2804	35.0354
20	2.0609	1.8252	2.201	3.6211	3.4615	5.7335	0.1465	-0.0675	-0.0835	0.4653	-0.0179	0.1001	0.3518	-0.0269	-0.1294	0.221	-0.0214	0.039	0.1564	0.0198	0.168	47.9694	-11.8112	41.2396
21	1.657	0.8924	2.288	1.9193	2.5692	8.0199	0.1089	-0.2427	0.1234	0.2925	-0.1429	0.3102	0.0316	-0.4529	0.0485	0.1841	-0.0158	0.0737	0.1895	-0.0391	0.1943	44.2933	-0.652	42.8398
22	0.3938	1.1417	0.8829	3.3059	2.5578	1.9784	0.0006	-0.3896	0.3324	0.205	-0.4544	0.956	0.045	-0.5745	0.391	0.202	-0.0119	0.0429	0.2956	-0.1	0.354	40.7203	4.0694	41.5267

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 44 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 45 through 67 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 68 through 123 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 124 through 140 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 141 through 162 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 163 through 214 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 215 through 247 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 248 through 268 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 269 through 297 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 13 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 14 through 44 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 45 through 67 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 68 through 79 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 80 through 107 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 108 through 123 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 124 through 140 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 141 through 162 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 163 through 214 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 215 through 247 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 248 through 268 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 269 through 289 )

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