PDB-8rah: Crystal structure of class Ie ribonucleotide reductase R2 subunit...

ID or keywords:

Entry

Database: PDB / ID: 8rah

Title

Crystal structure of class Ie ribonucleotide reductase R2 subunit with post-translational modification of Y150 into a DOPA from Gardnerella vaginalis

Components

ribonucleoside-diphosphate reductase

Keywords

OXIDOREDUCTASE / Ribonucleotide reductase R2e / Class Ie RNR / ferritin-like superfamily / NrdF / RNR beta-subunit

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
Similarity search - Function

Biological species

Gardnerella vaginalis ATCC 14019 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

John, J. / Hogbom, M.

Funding support

Sweden, 2items

Citation

Journal: Commun Biol / Year: 2025
Title: Characterization of a second class Ie ribonucleotide reductase.
Authors: John, J. / Lundin, D. / Branca, R.M. / Kumar, R. / Srinivas, V. / Lebrette, H. / Hogbom, M.

History

Deposition	Dec 1, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 11, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 5, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8rah.cif.gz	659.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8rah.ent.gz	456.3 KB	Display	PDB format
PDBx/mmJSON format	8rah.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ra/8rah ftp://data.pdbj.org/pub/pdb/validation_reports/ra/8rah	HTTPS FTP

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Related structure data

Related structure data	8ragC C: citing same article (ref.)
Similar structure data	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 (5)

Deposited unit

A: ribonucleoside-diphosphate reductase

B: ribonucleoside-diphosphate reductase

C: ribonucleoside-diphosphate reductase

D: ribonucleoside-diphosphate reductase

171 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ribonucleoside-diphosphate reductase

C: ribonucleoside-diphosphate reductase

defined by author
Evidence: homology
85.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ribonucleoside-diphosphate reductase

D: ribonucleoside-diphosphate reductase

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

Unit cell

Length a, b, c (Å)	173.710, 173.710, 157.890
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

#1: Protein	ribonucleoside-diphosphate reductase Mass: 42844.707 Da / Num. of mol.: 4 / Mutation: Y151DAH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gardnerella vaginalis ATCC 14019 (bacteria) Gene: HMPREF0421_21333 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E3D8A3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.09 Å³/Da / Density % sol: 69.9 % / Description: transparent rhombohedron
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus G4 condition (0.1 M Carboxylic acids, 0.1 M Buffer System 1 pH 6.5, 37.5% v/v Precipitant Mix 4) + 4% tert-butanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97622 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97622 Å / Relative weight: 1
Reflection	Resolution: 1.9→49.68 Å / Num. obs: 215066 / % possible obs: 99.63 % / Redundancy: 16.9 % / B_iso Wilson estimate: 45.56 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.1316 / R_pim(I) all: 0.03279 / R_rim(I) all: 0.1357 / Net I/σ(I): 13.2
Reflection shell	Resolution: 1.9→1.968 Å / Redundancy: 13.7 % / R_merge(I) obs: 4.584 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 21342 / CC_1/2: 0.271 / CC star: 0.653 / R_pim(I) all: 1.275 / R_rim(I) all: 4.761 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→49.68 Å / SU ML: 0.2844 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1892	1839	0.86 %
R_work	0.171	212458	-
obs	0.1712	214297	99.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 51.91 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→49.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10562	0	0	754	11316

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0069	10950
X-RAY DIFFRACTION	f_angle_d	0.7585	14875
X-RAY DIFFRACTION	f_chiral_restr	0.0466	1631
X-RAY DIFFRACTION	f_plane_restr	0.0082	1921
X-RAY DIFFRACTION	f_dihedral_angle_d	13.0992	4085

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 (%)
1.9-1.95	0.4367	136	0.405	15586	X-RAY DIFFRACTION	95.62
1.95-2.01	0.3188	142	0.3361	16252	X-RAY DIFFRACTION	99.92
2.01-2.07	0.3178	142	0.2813	16271	X-RAY DIFFRACTION	99.95
2.07-2.15	0.2186	137	0.2474	16288	X-RAY DIFFRACTION	99.98
2.15-2.23	0.2585	141	0.2309	16310	X-RAY DIFFRACTION	99.98
2.23-2.34	0.2294	137	0.1909	16288	X-RAY DIFFRACTION	99.98
2.34-2.46	0.19	142	0.1744	16339	X-RAY DIFFRACTION	99.99
2.46-2.61	0.2037	140	0.1705	16421	X-RAY DIFFRACTION	99.98
2.61-2.81	0.1951	142	0.1771	16353	X-RAY DIFFRACTION	100
2.81-3.1	0.1781	143	0.1834	16450	X-RAY DIFFRACTION	100
3.1-3.55	0.1977	142	0.1673	16448	X-RAY DIFFRACTION	100
3.55-4.47	0.1553	145	0.1407	16537	X-RAY DIFFRACTION	100
4.47-49.68	0.1703	150	0.1473	16915	X-RAY DIFFRACTION	99.91

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	1.11720780128	-0.495508158079	0.34552208365	2.27467237226	-0.108630344617	1.79816146263	-0.0500738613346	0.216695546606	-0.181835566248	-0.249603649775	-0.036355840223	0.205475825595	0.173318509729	-0.117512570227	0.0703608941694	0.554903661402	-0.118833933543	0.0183596994672	0.378038422898	-0.0263659009866	0.429469086357	75.523	-29.945	-84.06
2	1.22566346902	0.667702321826	1.89568467546	2.36891585532	1.34776107776	6.89180850607	-0.00708993898855	-0.0776681888704	-0.01293193305	0.201230952844	0.00617385808642	-0.0374019717716	-0.140236062465	-0.0141484293821	-0.0115124395286	0.36328281674	0.00318364224495	0.0973712957904	0.273863872209	0.00502806749416	0.328521262738	82.514	-20.511	-51.898
3	0.645425581552	0.260399280939	0.483067771911	0.931842494634	0.112061655278	1.88128986149	-0.0790097460665	0.00108420789799	-0.056203665663	0.134139029607	0.0696664086819	0.035763972496	-0.0276759873828	0.0493867704642	0.00928573574113	0.485303156977	0.00066481378641	0.0682741381436	0.35572953342	-0.00317765653553	0.427801919496	83.088	-26.889	-54.422
4	0.92540538243	0.568261280017	0.397686965173	2.0283672435	0.510802371934	1.87852120795	-0.0431828005107	-0.0407430510975	-0.040074227319	0.144749253316	-0.0110820081283	0.248820222371	-0.00117241391437	-0.253080747551	0.0487257636685	0.44471965723	0.0129665958746	0.0917548186961	0.410025856852	-0.0108178959737	0.440302049666	69.067	-26.594	-54.225
5	3.76548252738	2.18241701001	3.7237239425	2.65092433337	2.78955790861	6.31892178526	0.0864451459486	-0.644093833967	0.138846382064	0.536572640117	-0.157469508022	0.370965471015	0.133061599825	-0.680638968593	0.135077601993	0.587780227303	0.0413787529007	0.172711157844	0.560311538077	-0.0331554603684	0.522810006073	64.316	-22.475	-44.019
6	1.53343677568	1.03444388814	-0.0838984895804	2.72490189541	0.193926944594	2.04667644265	-0.210981313342	0.523746811541	-0.0440015179294	-0.274463463172	0.210200306733	-0.204201345022	-0.153025653701	0.378685540134	-0.0165040662761	0.444029433172	-0.198372535811	0.027269007781	0.710437293846	-0.0139044257308	0.410009543738	70.837	-63.867	-111.105
7	3.14640031338	0.940008301252	-3.07539872612	0.987800269686	0.219144776529	6.91790837003	0.0989480621124	-0.160689136924	0.0266592629544	0.118519234361	-0.0972008293578	0.0487423501	-0.00255961707026	0.0354154415957	-0.004197336153	0.397395597304	-0.0527470002212	-0.0287722827861	0.331327879913	0.0462944058104	0.390286199645	59.16	-65.265	-78.782
8	1.16904698171	0.332395725493	-0.0546769844467	0.77397112713	0.42521768962	1.00989323936	0.0533835293213	-0.0259137336467	0.0457416088028	0.0789433186692	-0.0175774291087	-0.0445676327241	0.0385851957502	-0.0469152021974	-0.0325798119146	0.46771085791	-0.0984658742652	-0.00360853169332	0.419945290084	0.0168881367572	0.437153184619	63.202	-60.295	-81.07
9	2.45361302951	0.777180538404	-0.87252770402	0.766983397896	-0.217352998379	2.27170073012	0.0331285824927	-0.104573003562	-0.174005821268	0.128744095699	-0.0599037318633	-0.110808730257	0.195478974776	0.0481308317835	0.0292068571635	0.46752204659	-0.0354194072857	-0.0370085250839	0.340935817548	0.0355045905822	0.417808155588	73.097	-70.728	-81.052
10	7.56690590704	-0.336941514633	-5.73020751109	2.8537256823	-1.0843287314	7.67357135431	0.0202347177766	-0.884246659604	-0.485382174775	0.48061856024	0.0558363189589	-0.0121205732516	0.360108276473	0.384727547501	-0.0433906020684	0.570837647169	-0.079343904637	-0.091038645493	0.469575020195	0.116619476189	0.462601356926	73.14	-76.899	-70.654
11	0.929420775892	-0.220676804903	0.613596090925	1.09243289852	0.475389394798	2.1168853838	0.00279531656484	-0.0887659775752	-0.175399891959	0.100521141709	-0.0121189525958	0.0123903554805	0.203369470719	0.0693690831183	-0.00845394754707	0.469798333818	0.00262812528193	0.052069740651	0.3200444324	-0.0275442398881	0.396202519675	86.84	-34.765	-55.837
12	0.772076364961	-0.50665018897	0.90454762881	3.18524658141	-1.97024575898	4.25136181508	-0.0603918963387	0.0980715970265	-0.0030061589373	-0.418171684561	0.0304832207438	0.0731816021525	0.0785919613164	0.0663855758822	0.0273566454193	0.471142670984	-0.086210428469	0.0463430602768	0.349160156219	-0.0390419174408	0.348316331776	83.15	-16.181	-84.032
13	0.245199929199	-0.0145047796791	0.0337839389037	1.05236499499	-0.487377341196	1.76726825036	-0.0802742124737	0.07821597388	-0.0644051288713	-0.249717737924	0.0682670123056	0.150822216781	-0.0335811824693	-0.0521490093062	0.0078548706851	0.583024851919	-0.0863189137809	0.02684030545	0.410731121597	-0.0501275267384	0.432264688321	80.993	-22.706	-83.273
14	0.695684026541	-0.941501651529	0.392369292706	3.34631786371	-0.935799492938	1.87816983031	-0.0625455718745	0.0111726206725	0.00491613284836	-0.139734785521	0.0838971650418	-0.0342516197154	-0.13437917936	0.265537962735	-0.00992933094791	0.487626260509	-0.0977258784253	0.0695528134606	0.428990366664	-0.0475772439515	0.369878103046	93.813	-20.993	-81.633
15	3.65477164497	-3.24734065992	4.59294453024	5.19201733704	-5.25184891126	9.67115575232	0.188733290806	0.297322197449	-0.164252314204	-0.550031720005	-0.229286852715	-0.21963034811	0.531085307426	0.607669128144	0.0182873190672	0.629302523908	-0.05337512452	0.135961177763	0.491687554016	-0.0960876881473	0.410524616465	96.874	-35.295	-88.23
16	3.74491194447	-3.97948113266	2.39194505799	5.99855413102	-4.10192216412	3.78177843844	0.283479403619	0.606220580824	0.35610156291	-0.78746140484	-0.357689862714	-0.546119043548	0.256608992187	0.747056692727	0.0739332495219	0.703749965172	-0.137518450396	0.179581091273	0.628011138104	-0.0359943153044	0.471281024643	100.391	-20.085	-93.003
17	1.33753496684	0.428504013683	-0.623758114382	1.27724816164	0.511305291053	1.65188808935	0.0340822374859	-0.135170214133	0.240986061364	0.0778689383145	-0.0209446452177	-0.0879140141735	-0.115481451322	0.0136120910809	-0.0285599051842	0.430711085917	-0.0741273499555	0.0194874751359	0.360447547606	0.0409232134397	0.425058554615	66.703	-52.222	-82.489
18	2.03588712179	1.81950061372	1.03453095894	3.37788000587	2.71767820195	4.86779814328	-0.263754835505	0.354064901312	-0.0885406998689	-0.332457990742	0.170745737224	-0.0642889393832	-0.181454357595	0.0747708497967	0.0862953757058	0.374224122438	-0.086710232361	0.0149800093378	0.508082981888	0.0373132902007	0.356279455019	55.854	-67.995	-110.919
19	1.28256874392	0.641356390971	0.135317469674	1.0360623267	0.49510630311	1.26223368622	-0.243078661568	0.448881765395	-0.0791595367944	-0.240464091523	0.256038996907	-0.0559516833108	-0.0536682463926	0.189882534969	-0.0400451994997	0.481327006639	-0.14589294491	0.036939497702	0.614768975946	0.0289409049888	0.382877849988	62.001	-64.913	-110.181
20	1.56297797877	1.35277102007	0.373049574605	1.5660676831	0.57091446528	1.61336834954	-0.183529048267	0.264970682799	0.155302130041	-0.179601854107	0.090512280952	0.0966332656945	-0.269082668891	-0.100069459556	0.0753994650809	0.505832810172	-0.077343164169	-0.0269957596443	0.549931653295	0.0855816211112	0.420631678309	51.986	-56.855	-108.536
21	1.71457349207	0.937732321609	0.25522586872	7.92665989547	6.09601547984	7.14728641217	-0.299531474213	0.43451744462	0.38549123584	-1.0639693468	0.184070845116	-0.149927847234	-1.19941897255	0.177909979099	0.10929469246	0.750722158793	-0.216410877235	-0.111886459823	0.63138231094	0.205999599017	0.497386079129	59.628	-44.718	-115.262
22	2.35233867965	1.67294591384	1.20170550348	7.22126401331	4.35777781024	5.34674495779	-0.390238999478	0.591528303114	0.259794572053	-1.12200720606	0.115111405194	0.539519163837	-0.90390355897	-0.297776047995	0.26465249922	0.678644717458	-0.101771305337	-0.140576883347	0.680798813113	0.147730197006	0.473683101128	46.529	-53.194	-120.094

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 8:73 )	A	8 - 73
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 74:129 )	A	74 - 129
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 130:188 )	A	130 - 188
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 189:285 )	A	189 - 285
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 286:332 )	A	286 - 332
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 8:73 )	B	8 - 73
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 74:129 )	B	74 - 129
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 130:188 )	B	130 - 188
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 189:285 )	B	189 - 285
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 286:332 )	B	286 - 332
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 8:73 )	C	8 - 73
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 74:129 )	C	74 - 129
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 130:188 )	C	130 - 188
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 189:254 )	C	189 - 254
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 255:285 )	C	255 - 285
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 286:332 )	C	286 - 332
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 8:73 )	D	8 - 73
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 74:129 )	D	74 - 129
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 130:188 )	D	130 - 188
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 189:254 )	D	189 - 254
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 255:285 )	D	255 - 285
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 286:332 )	D	286 - 332

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