PDB-7q3c: Ribonucleotide Reductase AaR2 protein from Aquifex aeolicus

ID or keywords:

Entry

Database: PDB / ID: 7q3c

Title

Ribonucleotide Reductase AaR2 protein from Aquifex aeolicus

Components

Ribonucleoside-diphosphate reductase subunit beta

Keywords

OXIDOREDUCTASE / ribonucleotide reductase / R2 subunit

Function / homology

:

Function and homology information

Biological species

Aquifex aeolicus VF5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Scaletti, E.R. / Rehling, D. / Stenmark, P.

Funding support

Sweden, 2items

Citation

Journal: Biochemistry / Year: 2022
Title: Structural and Biochemical Investigation of Class I Ribonucleotide Reductase from the Hyperthermophile Aquifex aeolicus.
Authors: Rehling, D. / Scaletti, E.R. / Rozman Grinberg, I. / Lundin, D. / Sahlin, M. / Hofer, A. / Sjoberg, B.M. / Stenmark, P.

History

Deposition	Oct 27, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7q3c.cif.gz	86 KB	Display	PDBx/mmCIF format
PDB format	pdb7q3c.ent.gz		Display	PDB format
PDBx/mmJSON format	7q3c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7q3c_validation.pdf.gz	780.3 KB	Display	wwPDB validaton report
Full document	7q3c_full_validation.pdf.gz	784.6 KB	Display
Data in XML	7q3c_validation.xml.gz	13.9 KB	Display
Data in CIF	7q3c_validation.cif.gz	18.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/7q3c ftp://data.pdbj.org/pub/pdb/validation_reports/q3/7q3c	HTTPS FTP

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Related structure data

Related structure data	7agjC 7aikC 7ailSC 7q39C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&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 (1)

Deposited unit

AAA: Ribonucleoside-diphosphate reductase subunit beta

hetero molecules

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

1

AAA: Ribonucleoside-diphosphate reductase subunit beta

hetero molecules

AAA: Ribonucleoside-diphosphate reductase subunit beta

hetero molecules

defined by author&software
Evidence: gel filtration
84.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.183, 69.183, 177.500
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Ribonucleoside-diphosphate reductase subunit beta Mass: 42113.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.52 Å³/Da / Density % sol: 51.22 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M citrate pH 4.0, 1.0 M lithium chloride, 20 % PEG6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.15→48.968 Å / Num. obs: 24392 / % possible obs: 100 % / Redundancy: 25.1 % / CC_1/2: 1 / Net I/σ(I): 24.6
Reflection shell	Resolution: 2.15→2.22 Å / Num. unique obs: 2058 / CC_1/2: 0.69

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7AIL

7ail

Resolution: 2.15→48.968 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.894 / WR_factor R_free: 0.279 / WR_factor R_work: 0.217 / SU B: 9.207 / SU ML: 0.229 / Average fsc free: 0.8158 / Average fsc work: 0.8352 / Cross valid method: FREE R-VALUE / ESU R: 0.259 / ESU R Free: 0.238
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3145	1203	4.948 %
R_work	0.2471	23110	-
all	0.25	-	-
obs	-	24313	99.975 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 61.901 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.08 Å²	-0 Å²	-0 Å²
2-	-	1.08 Å²	0 Å²
3-	-	-	-2.16 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→48.968 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2667	0	1	84	2752

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	2743
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2544
X-RAY DIFFRACTION	r_angle_refined_deg	1.194	1.646	3720
X-RAY DIFFRACTION	r_angle_other_deg	1.118	1.575	5827
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.752	5	321
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.617	22.892	166
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.717	15	472
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.513	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	354
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3128
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	694
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	647
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	2452
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	1362
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	1261
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	112
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.077	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.186	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.181	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.157	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	3.072	6.559	1284
X-RAY DIFFRACTION	r_mcbond_other	3.069	6.558	1283
X-RAY DIFFRACTION	r_mcangle_it	4.602	9.828	1605
X-RAY DIFFRACTION	r_mcangle_other	4.601	9.83	1606
X-RAY DIFFRACTION	r_scbond_it	2.868	6.727	1458
X-RAY DIFFRACTION	r_scbond_other	2.867	6.728	1459
X-RAY DIFFRACTION	r_scangle_it	4.557	10.009	2115
X-RAY DIFFRACTION	r_scangle_other	4.556	10.011	2116
X-RAY DIFFRACTION	r_lrange_it	6.996	75.685	3274
X-RAY DIFFRACTION	r_lrange_other	6.924	75.654	3266

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 (%)
2.15-2.206	0.41	81	0.362	1662	X-RAY DIFFRACTION	100
2.206-2.266	0.371	67	0.369	1630	X-RAY DIFFRACTION	100
2.266-2.332	0.369	85	0.346	1606	X-RAY DIFFRACTION	99.8819
2.332-2.403	0.422	83	0.327	1520	X-RAY DIFFRACTION	99.9377
2.403-2.482	0.362	92	0.3	1481	X-RAY DIFFRACTION	99.9365
2.482-2.569	0.25	76	0.25	1466	X-RAY DIFFRACTION	100
2.569-2.666	0.331	72	0.287	1402	X-RAY DIFFRACTION	100
2.666-2.775	0.363	56	0.293	1367	X-RAY DIFFRACTION	100
2.775-2.898	0.365	79	0.298	1281	X-RAY DIFFRACTION	100
2.898-3.039	0.413	75	0.287	1250	X-RAY DIFFRACTION	100
3.039-3.203	0.372	59	0.309	1178	X-RAY DIFFRACTION	100
3.203-3.397	0.406	60	0.29	1140	X-RAY DIFFRACTION	100
3.397-3.63	0.282	63	0.267	1065	X-RAY DIFFRACTION	100
3.63-3.92	0.313	39	0.232	1009	X-RAY DIFFRACTION	100
3.92-4.293	0.269	60	0.206	927	X-RAY DIFFRACTION	100
4.293-4.797	0.25	46	0.178	836	X-RAY DIFFRACTION	100
4.797-5.534	0.28	43	0.208	755	X-RAY DIFFRACTION	100
5.534-6.765	0.255	26	0.226	670	X-RAY DIFFRACTION	100
6.765-9.515	0.26	30	0.178	526	X-RAY DIFFRACTION	100
9.515-48.968	0.397	11	0.237	340	X-RAY DIFFRACTION	99.4334

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