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- PDB-9r5l: Crystal structure of class Ie ribonucleotide reductase R2 subunit... -

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Basic information

Entry
Database: PDB / ID: 9r5l
TitleCrystal structure of class Ie ribonucleotide reductase R2 subunit from Mesoplasma florum with a D212N mutation
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 / metal ion binding
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 speciesMesoplasma florum L1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJohn, J. / Hogbom, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2021-03992 Sweden
Knut and Alice Wallenberg Foundation2023.0201 Sweden
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Low-barrier hydrogen bond powers long-range radical transfer in the metal-free ribonucleotide reductase.
Authors: Sirohiwal, A. / John, J. / Kutin, Y. / Kumar, R. / Baserga, F. / Srinivas, V. / Lebrette, H. / Poverlein, M.C. / Gamiz-Hernandez, A.P. / Heberle, J. / Kasanmascheff, M. / Hogbom, M. / Kaila, V.R.I.
History
DepositionMay 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribonucleoside-diphosphate reductase


Theoretical massNumber of molelcules
Total (without water)39,8281
Polymers39,8281
Non-polymers00
Water3,225179
1
A: ribonucleoside-diphosphate reductase

A: ribonucleoside-diphosphate reductase


Theoretical massNumber of molelcules
Total (without water)79,6552
Polymers79,6552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5520 Å2
ΔGint-38 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.083, 45.774, 56.833
Angle α, β, γ (deg.)90.000, 112.221, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

21A-452-

HOH

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Components

#1: Protein ribonucleoside-diphosphate reductase


Mass: 39827.625 Da / Num. of mol.: 1 / Mutation: D212N
Source method: isolated from a genetically manipulated source
Details: N-terminal tag, additional residues after cleavage: GHMAS
Source: (gene. exp.) Mesoplasma florum L1 (bacteria) / Gene: Mfl530 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6F0T5, ribonucleoside-diphosphate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM ammonium sulfate, 12-16% PEG 3350, 100-200 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→43.2 Å / Num. obs: 36454 / % possible obs: 97.81 % / Redundancy: 7 % / Biso Wilson estimate: 28.89 Å2 / CC1/2: 0.713 / CC star: 1 / Rmerge(I) obs: 0.05782 / Rpim(I) all: 0.02348 / Rrim(I) all: 0.06248 / Net I/σ(I): 13.09
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.316 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 2704 / CC1/2: 0.713 / CC star: 0.912 / Rpim(I) all: 0.5339 / Rrim(I) all: 1.426 / % possible all: 96.43

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→43.2 Å / SU ML: 0.2865 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.9578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2567 1818 4.99 %
Rwork0.2111 34592 -
obs0.2133 36410 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 0 179 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592672
X-RAY DIFFRACTIONf_angle_d0.74673640
X-RAY DIFFRACTIONf_chiral_restr0.0479397
X-RAY DIFFRACTIONf_plane_restr0.0087467
X-RAY DIFFRACTIONf_dihedral_angle_d13.1675997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.48541550.45312573X-RAY DIFFRACTION96.43
1.75-1.80.46061330.41422618X-RAY DIFFRACTION96.7
1.8-1.860.4151380.3712630X-RAY DIFFRACTION96.85
1.86-1.920.37261380.33162639X-RAY DIFFRACTION97.34
1.92-20.37651440.29422605X-RAY DIFFRACTION97.38
2-2.090.33561160.27182666X-RAY DIFFRACTION97.75
2.09-2.20.2841420.24692639X-RAY DIFFRACTION97.68
2.2-2.340.26911500.21412640X-RAY DIFFRACTION97.86
2.34-2.520.23671390.21062691X-RAY DIFFRACTION98.3
2.52-2.770.28431340.21242666X-RAY DIFFRACTION98.56
2.77-3.170.26911540.20932700X-RAY DIFFRACTION98.86
3.17-40.23861290.18112739X-RAY DIFFRACTION99.07
4-43.20.18761460.16092786X-RAY DIFFRACTION98.75

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