PDB-7q39: Ribonucleotide Reductase R2_genomic protein from Aquifex aeolicus

ID or keywords:

Entry

Database: PDB / ID: 7q39

Title

Ribonucleotide Reductase R2_genomic protein from Aquifex aeolicus

Components

Ribonucleoside-diphosphate reductase subunit beta

Keywords

OXIDOREDUCTASE / ribonucletotide reductase / R2 subunit

Function / homology

:

Function and homology information

Biological species

Aquifex aeolicus VF5 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Scaletti, E. / 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

-
Download

PDBx/mmCIF format	7q39.cif.gz	86.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7q39.ent.gz		Display	PDB format
PDBx/mmJSON format	7q39.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7q39_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7q39_full_validation.pdf.gz	1.3 MB	Display
Data in XML	7q39_validation.xml.gz	14.2 KB	Display
Data in CIF	7q39_validation.cif.gz	19 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/7q39 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/7q39	HTTPS FTP

-
Related structure data

Related structure data	7agjC 7aikC 7ailSC 7q3cC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

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
Evidence: gel filtration
84.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.246, 69.246, 177.570
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.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.33 %
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

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 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: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.1→47.247 Å / Num. obs: 26173 / % possible obs: 100 % / Redundancy: 25.7 % / CC_1/2: 1 / Net I/σ(I): 22.9
Reflection shell	Resolution: 2.1→2.16 Å / Num. unique obs: 2084 / CC_1/2: 0.673

-
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: 2.1→47.247 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.941 / SU B: 9.658 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.212
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2973	1284	4.921 %
R_work	0.2378	24809	-
all	0.241	-	-
obs	-	26093	99.977 %

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: 62.164 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.57 Å²	0 Å²	0 Å²
2-	-	1.57 Å²	0 Å²
3-	-	-	-3.141 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→47.247 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2662	0	2	69	2733

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	2756
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2529
X-RAY DIFFRACTION	r_angle_refined_deg	1.352	1.645	3745
X-RAY DIFFRACTION	r_angle_other_deg	1.221	1.573	5798
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.495	5	325
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.143	23.214	168
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.707	15	467
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.102	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	356
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3167
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	693
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	782
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	2560
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1374
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	1311
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.215	0.2	112
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.051	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.054	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.149	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.176	0.2	76
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.221	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	4.65	6.6	1294
X-RAY DIFFRACTION	r_mcbond_other	4.651	6.598	1293
X-RAY DIFFRACTION	r_mcangle_it	6.791	9.884	1621
X-RAY DIFFRACTION	r_mcangle_other	6.789	9.887	1622
X-RAY DIFFRACTION	r_scbond_it	4.444	6.785	1461
X-RAY DIFFRACTION	r_scbond_other	4.442	6.787	1462
X-RAY DIFFRACTION	r_scangle_it	6.778	10.084	2124
X-RAY DIFFRACTION	r_scangle_other	6.777	10.085	2125
X-RAY DIFFRACTION	r_lrange_it	9.598	78.344	3417
X-RAY DIFFRACTION	r_lrange_other	9.553	78.292	3409

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 (%)
2.1-2.155	0.355	87	0.392	1771	X-RAY DIFFRACTION	100
2.155-2.213	0.449	98	0.362	1740	X-RAY DIFFRACTION	99.9456
2.213-2.278	0.51	79	0.372	1718	X-RAY DIFFRACTION	99.9444
2.278-2.348	0.436	82	0.353	1655	X-RAY DIFFRACTION	100
2.348-2.424	0.36	89	0.339	1598	X-RAY DIFFRACTION	100
2.424-2.509	0.366	83	0.311	1562	X-RAY DIFFRACTION	100
2.509-2.604	0.327	93	0.31	1487	X-RAY DIFFRACTION	100
2.604-2.71	0.374	66	0.31	1466	X-RAY DIFFRACTION	100
2.71-2.83	0.439	59	0.303	1397	X-RAY DIFFRACTION	100
2.83-2.968	0.296	68	0.292	1364	X-RAY DIFFRACTION	100
2.968-3.129	0.358	79	0.29	1261	X-RAY DIFFRACTION	100
3.129-3.318	0.306	63	0.273	1225	X-RAY DIFFRACTION	100
3.318-3.546	0.343	68	0.27	1118	X-RAY DIFFRACTION	100
3.546-3.829	0.356	48	0.241	1100	X-RAY DIFFRACTION	100
3.829-4.193	0.221	51	0.211	990	X-RAY DIFFRACTION	100
4.193-4.686	0.208	42	0.164	923	X-RAY DIFFRACTION	100
4.686-5.406	0.264	54	0.169	801	X-RAY DIFFRACTION	100
5.406-6.609	0.243	31	0.193	708	X-RAY DIFFRACTION	100
6.609-9.298	0.213	29	0.161	566	X-RAY DIFFRACTION	100
9.298-47.247	0.247	15	0.173	359	X-RAY DIFFRACTION	98.9418

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi