PDB-5im3: Crystal structure of the class I ribonucleotide reductase from Ps...

ID or keywords:

Entry

Database: PDB / ID: 5im3

Title

Crystal structure of the class I ribonucleotide reductase from Pseudomonas aeruginosa in complex with dATP

Components

Ribonucleoside-diphosphate reductase

Keywords

OXIDOREDUCTASE / allosteric regulation / ten-stranded alpha-beta barrel / ATP cone

Function / homology

Function and homology information

ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / ATP binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.298 Å

Authors

Johansson, R. / Logan, D.T.

Funding support

Sweden, 1items

Citation

Journal: Structure / Year: 2016
Title: Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones.
Authors: Johansson, R. / Jonna, V.R. / Kumar, R. / Nayeri, N. / Lundin, D. / Sjoberg, B.M. / Hofer, A. / Logan, D.T.

History

Deposition	Mar 5, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 11, 2016	Group: Database references
Revision 1.2	Jun 15, 2016	Group: Database references
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5im3.cif.gz	704.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5im3.ent.gz	583.6 KB	Display	PDB format
PDBx/mmJSON format	5im3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5im3_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	5im3_full_validation.pdf.gz	2.4 MB	Display
Data in XML	5im3_validation.xml.gz	60 KB	Display
Data in CIF	5im3_validation.cif.gz	82.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/im/5im3 ftp://data.pdbj.org/pub/pdb/validation_reports/im/5im3	HTTPS FTP

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Related structure data

Related structure data	2zlfS S: Starting model for refinement
Similar structure data	20908 6uvn-d 1i84-d 20349 20350 20351 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	#238 - Oct 2019 Ribonucleotide Reductase similarity (13) #177 - Sep 2014 Apoptosomes similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Ribonucleoside-diphosphate reductase

B: Ribonucleoside-diphosphate reductase

hetero molecules

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

1

A: Ribonucleoside-diphosphate reductase

B: Ribonucleoside-diphosphate reductase

hetero molecules

A: Ribonucleoside-diphosphate reductase

B: Ribonucleoside-diphosphate reductase

hetero molecules

defined by author&software
435 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	267.465, 62.577, 173.761
Angle α, β, γ (deg.)	90.00, 127.81, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Ribonucleoside-diphosphate reductase Mass: 107231.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: nrdA, PA1156 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9I4I1, ribonucleoside-diphosphate reductase
#2: Chemical	ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE Mass: 491.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.68 Å³/Da / Density % sol: 54.08 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 1 microlitre of protein at 10 or 20 mg/ml in 50 mM Tris-HCl, pH 7.5, 2 mM DTT, 2 mM dATP was mixed with 1 microlitre of a reservoir solution consisting of 0.1 M acetic acid pH 4.7 and 6% PEG 4000.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2013
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.298→46.1 Å / Num. obs: 100813 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / B_iso Wilson estimate: 42.1 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.058 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.298→2.44 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.537 / Mean I/σ(I) obs: 2.1 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2328: ???)	refinement
XDS	2013	data reduction
Aimless	0.5.9	data scaling
PHASER	2.3.0	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZLF

2zlf

Resolution: 2.298→46.085 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.217	5059	5.02 %	random
R_work	0.1859	-	-	-
obs	0.1874	100795	98.93 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.298→46.085 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13751	0	182	256	14189

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	14230
X-RAY DIFFRACTION	f_angle_d	0.616	19324
X-RAY DIFFRACTION	f_dihedral_angle_d	11.703	8592
X-RAY DIFFRACTION	f_chiral_restr	0.041	2149
X-RAY DIFFRACTION	f_plane_restr	0.003	2542

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 (%)
2.298-2.3241	0.311	166	0.2783	2862	X-RAY DIFFRACTION	89
2.3241-2.3514	0.2954	187	0.2582	3115	X-RAY DIFFRACTION	100
2.3514-2.3801	0.295	160	0.2585	3225	X-RAY DIFFRACTION	100
2.3801-2.4102	0.278	146	0.2487	3218	X-RAY DIFFRACTION	100
2.4102-2.442	0.2705	180	0.2482	3119	X-RAY DIFFRACTION	99
2.442-2.4754	0.2749	137	0.2351	3265	X-RAY DIFFRACTION	100
2.4754-2.5108	0.2288	177	0.2215	3187	X-RAY DIFFRACTION	100
2.5108-2.5482	0.2629	180	0.224	3163	X-RAY DIFFRACTION	100
2.5482-2.5881	0.2581	159	0.2236	3222	X-RAY DIFFRACTION	100
2.5881-2.6305	0.2986	163	0.2177	3192	X-RAY DIFFRACTION	100
2.6305-2.6758	0.2618	144	0.2155	3245	X-RAY DIFFRACTION	100
2.6758-2.7245	0.2426	166	0.2137	3201	X-RAY DIFFRACTION	100
2.7245-2.7769	0.2324	166	0.2056	3132	X-RAY DIFFRACTION	99
2.7769-2.8336	0.229	183	0.2033	3225	X-RAY DIFFRACTION	100
2.8336-2.8952	0.2119	165	0.2052	3165	X-RAY DIFFRACTION	99
2.8952-2.9625	0.237	162	0.212	3197	X-RAY DIFFRACTION	99
2.9625-3.0366	0.2521	166	0.22	3186	X-RAY DIFFRACTION	99
3.0366-3.1186	0.2713	176	0.2099	3242	X-RAY DIFFRACTION	99
3.1186-3.2104	0.2649	185	0.2204	3146	X-RAY DIFFRACTION	100
3.2104-3.314	0.2812	170	0.213	3215	X-RAY DIFFRACTION	100
3.314-3.4324	0.2246	182	0.207	3192	X-RAY DIFFRACTION	99
3.4324-3.5698	0.2402	177	0.2057	3182	X-RAY DIFFRACTION	100
3.5698-3.7322	0.1962	160	0.1838	3207	X-RAY DIFFRACTION	99
3.7322-3.9288	0.2002	161	0.1729	3235	X-RAY DIFFRACTION	99
3.9288-4.1749	0.1809	199	0.158	3183	X-RAY DIFFRACTION	99
4.1749-4.4969	0.182	171	0.1466	3208	X-RAY DIFFRACTION	99
4.4969-4.949	0.1696	158	0.1402	3229	X-RAY DIFFRACTION	99
4.949-5.664	0.172	169	0.16	3245	X-RAY DIFFRACTION	99
5.664-7.1318	0.2203	160	0.1691	3257	X-RAY DIFFRACTION	99
7.1318-46.0942	0.1708	184	0.1425	3276	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	4.0089	0.9547	3.2024	2.9427	-0.5041	3.9064	-0.4781	-0.2498	0.5541	-0.2649	0.1495	0.239	-1.5815	-0.4298	0.2936	0.939	0.0381	-0.0661	0.5578	-0.1086	0.4796	48.8021	23.0633	0.2875
2	3.075	2.5394	-1.9806	2.4505	-1.9536	1.4727	-0.1899	0.0057	-0.0976	0.0065	-0.01	-0.5398	-0.3362	0.3334	0.2319	0.5363	-0.1755	-0.0526	0.9573	0.0953	0.687	40.6637	3.5516	42.9746
3	3.1361	1.412	1.7401	1.6528	0.6663	1.8593	-0.0368	-0.4703	-0.1296	0.1801	-0.0153	-0.3575	-0.0833	0.2184	0.0305	0.339	0.0201	-0.0404	0.8324	0.1655	0.5046	22.4304	-14.9983	53.4597
4	1.3288	0.6309	0.0807	5.3791	2.4932	4.8803	-0.1138	-0.211	-0.0021	-0.0667	-0.001	0.2506	0.0792	-0.2863	0.037	0.2137	0.0282	0.018	0.545	0.12	0.2846	-10.2842	-19.8699	35.6007
5	2.0812	0.3532	0.4787	1.1003	0.0296	1.1183	-0.0478	-0.0982	-0.4853	-0.1277	0.0225	-0.35	0.1491	0.1507	0.0162	0.341	0.0128	0.102	0.4937	0.1026	0.4894	7.4044	-33.3178	34.1825
6	5.1094	3.0245	-1.2327	2.6383	-1.1231	2.5242	-0.2682	0.302	-0.3099	-0.3708	0.0726	-0.4817	-0.1099	0.2845	0.1901	0.4282	0.0355	0.1818	0.5561	0.033	0.4846	22.8825	-19.5933	21.2881
7	5.2136	0.5147	0.6876	7.8341	-1.6137	2.8724	-0.3198	0.2432	-0.3175	0.0818	0.2031	-0.345	0.4913	0.1944	0.1363	0.528	0.1443	0.0691	0.5078	-0.0572	0.247	-45.339	-2.094	-0.2092
8	1.5954	0.164	0.95	0.422	-0.0632	2.5712	0.1257	0.1041	-0.4568	-0.2911	-0.0298	0.0443	0.7589	-0.0179	-0.0825	0.6082	-0.0059	-0.0312	0.2168	-0.0262	0.459	-54.5553	-17.6988	35.3369
9	5.3465	2.2862	-0.8929	2.6325	-0.1701	1.365	-0.0886	0.1025	-0.2326	0.0615	0.0395	-0.1445	0.1274	0.5475	0.0322	0.2729	0.0615	-0.0067	0.5037	0.0758	0.2536	-18.9796	-9.1455	49.4644
10	2.5552	-0.3122	0.2644	3.4909	2.034	2.6591	0.0119	-0.0258	0.2717	-0.0042	-0.0318	-0.4033	-0.2233	0.5168	-0.0154	0.2918	-0.1312	-0.0385	0.6042	0.1322	0.3621	-11.6688	7.7482	49.3816
11	1.6722	-0.0063	0.5645	1.0433	-0.1718	1.6329	-0.0602	-0.092	0.1332	-0.0394	-0.0645	0.0553	-0.1624	0.1395	0.1139	0.2647	-0.0164	-0.0058	0.2093	-0.0119	0.2386	-39.8372	4.5331	50.9605
12	4.1283	0.038	1.6949	1.1462	0.2117	2.2369	-0.1645	0.2156	0.5936	-0.1612	-0.1196	-0.0126	-0.5598	0.1344	0.2773	0.4207	-0.035	-0.0457	0.207	0.0114	0.3657	-36.6827	15.7099	44.4496

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 32 through 138 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 139 through 253 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 254 through 381 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 382 through 466 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 467 through 772 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 773 through 912 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 30 through 134 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 135 through 362 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 363 through 415 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 416 through 539 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 540 through 841 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 842 through 910 )

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