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

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Basic information

Entry
Database: PDB / ID: 8rag
TitleCrystal structure of class Ie ribonucleotide reductase R2 subunit without Y150 modification from Gardnerella vaginalis
Componentsribonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE / 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
Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesGardnerella vaginalis ATCC 14019 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJohn, J. / Hogbom, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2021-03992 Sweden
Knut and Alice Wallenberg Foundation2019.0436 Sweden
CitationJournal: 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
DepositionDec 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribonucleoside-diphosphate reductase
B: ribonucleoside-diphosphate reductase
C: ribonucleoside-diphosphate reductase
D: ribonucleoside-diphosphate reductase


Theoretical massNumber of molelcules
Total (without water)167,0304
Polymers167,0304
Non-polymers00
Water21,5461196
1
A: ribonucleoside-diphosphate reductase
B: ribonucleoside-diphosphate reductase


Theoretical massNumber of molelcules
Total (without water)83,5152
Polymers83,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-58 kcal/mol
Surface area24570 Å2
MethodPISA
2
C: ribonucleoside-diphosphate reductase
D: ribonucleoside-diphosphate reductase


Theoretical massNumber of molelcules
Total (without water)83,5152
Polymers83,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-56 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.520, 173.520, 157.582
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
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

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Components

#1: Protein
ribonucleoside-diphosphate reductase


Mass: 41757.574 Da / Num. of mol.: 4
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, ribonucleoside-diphosphate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1196 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.8 % / Description: transparent rhombohedron
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.9→47.74 Å / Num. obs: 214258 / % possible obs: 99.95 % / Redundancy: 21 % / Biso Wilson estimate: 36.95 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1704 / Rpim(I) all: 0.03803 / Rrim(I) all: 0.1746 / Net I/σ(I): 12.94
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 2.239 / Mean I/σ(I) obs: 0.68 / Num. unique obs: 21312 / CC1/2: 0.596 / CC star: 0.864 / Rpim(I) all: 0.4927 / Rrim(I) all: 2.293

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.74 Å / SU ML: 0.1779 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1944 1450 0.68 %
Rwork0.1666 212726 -
obs0.1668 214176 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10607 0 0 1196 11803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006411112
X-RAY DIFFRACTIONf_angle_d0.742215111
X-RAY DIFFRACTIONf_chiral_restr0.04671650
X-RAY DIFFRACTIONf_plane_restr0.00841966
X-RAY DIFFRACTIONf_dihedral_angle_d12.86964137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.31771410.304521136X-RAY DIFFRACTION99.83
1.97-2.050.23861560.232821058X-RAY DIFFRACTION99.92
2.05-2.140.22451350.221421149X-RAY DIFFRACTION99.98
2.14-2.250.21421810.190821161X-RAY DIFFRACTION99.99
2.25-2.390.25721450.183621161X-RAY DIFFRACTION99.99
2.39-2.580.21111420.16521185X-RAY DIFFRACTION99.99
2.58-2.840.2251090.186921296X-RAY DIFFRACTION100
2.84-3.250.18891310.167221327X-RAY DIFFRACTION100
3.25-4.090.18691650.147821403X-RAY DIFFRACTION100
4.09-47.740.15481450.143421850X-RAY DIFFRACTION99.92

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