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- PDB-8bt4: Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, radi... -

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Basic information

Entry
Database: PDB / ID: 8bt4
TitleRibonucleotide Reductase class Ie R2 from Mesoplasma florum, radical-lost ground state
ComponentsRibonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase R2 subunit / Ferritin-like superfamily / DOPA post-translational modification
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 / 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 / FOURIER SYNTHESIS / Resolution: 1.35 Å
AuthorsLebrette, H. / Srinivas, V. / Hogbom, M.
Funding support Sweden, European Union, 4items
OrganizationGrant numberCountry
Swedish Research Council2021-03992 Sweden
European Research Council (ERC)HIGH-GEAR 724394European Union
Knut and Alice Wallenberg Foundation2017.0275 Sweden
Knut and Alice Wallenberg Foundation2019.0436 Sweden
CitationJournal: Science / Year: 2023
Title: Structure of a ribonucleotide reductase R2 protein radical.
Authors: Lebrette, H. / Srinivas, V. / John, J. / Aurelius, O. / Kumar, R. / Lundin, D. / Brewster, A.S. / Bhowmick, A. / Sirohiwal, A. / Kim, I.S. / Gul, S. / Pham, C. / Sutherlin, K.D. / Simon, P. ...Authors: Lebrette, H. / Srinivas, V. / John, J. / Aurelius, O. / Kumar, R. / Lundin, D. / Brewster, A.S. / Bhowmick, A. / Sirohiwal, A. / Kim, I.S. / Gul, S. / Pham, C. / Sutherlin, K.D. / Simon, P. / Butryn, A. / Aller, P. / Orville, A.M. / Fuller, F.D. / Alonso-Mori, R. / Batyuk, A. / Sauter, N.K. / Yachandra, V.K. / Yano, J. / Kaila, V.R.I. / Sjoberg, B.M. / Kern, J. / Roos, K. / Hogbom, M.
History
DepositionNov 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: 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
B: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,41411
Polymers79,6892
Non-polymers7259
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-60 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.503, 53.369, 79.030
Angle α, β, γ (deg.)90.000, 108.379, 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

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Components

#1: Protein Ribonucleoside-diphosphate reductase / Ribonucleotide Reductase class Ie R2 subunit


Mass: 39844.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: post-translational modification of Y126 into a DOPA
Source: (gene. exp.) Mesoplasma florum L1 (bacteria) / Strain: ATCC 33453 / NBRC 100688 / NCTC 11704 / L1 / Gene: Mfl530 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6F0T5, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 175 mM calcium acetate, 100 mM ammonium sulphate and 20% (w/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→48.62 Å / Num. obs: 144603 / % possible obs: 94.89 % / Redundancy: 4.3 % / Biso Wilson estimate: 18.49 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.053 / Net I/σ(I): 14.72
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.88 / Num. unique obs: 13258 / CC1/2: 0.743 / Rrim(I) all: 0.939 / % possible all: 87.47

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIX1.19_4092refinement
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.35→48.62 Å / SU ML: 0.1511 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.7271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.164 7225 5 %
Rwork0.1433 137329 -
obs0.1444 144554 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.27 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 44 590 5708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00495641
X-RAY DIFFRACTIONf_angle_d0.74347694
X-RAY DIFFRACTIONf_chiral_restr0.0696818
X-RAY DIFFRACTIONf_plane_restr0.00661001
X-RAY DIFFRACTIONf_dihedral_angle_d12.33452113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.30792040.29433870X-RAY DIFFRACTION79.91
1.37-1.380.31052260.2724295X-RAY DIFFRACTION90.47
1.38-1.40.28432310.22764413X-RAY DIFFRACTION92.14
1.4-1.420.22542380.19234503X-RAY DIFFRACTION93.75
1.42-1.430.2352380.17424525X-RAY DIFFRACTION94.47
1.43-1.450.20492400.16554560X-RAY DIFFRACTION94.96
1.45-1.480.22842400.16484559X-RAY DIFFRACTION94.97
1.48-1.50.19012390.1564546X-RAY DIFFRACTION95.07
1.5-1.520.20212430.15154615X-RAY DIFFRACTION95.16
1.52-1.550.19492380.15424510X-RAY DIFFRACTION95.09
1.55-1.570.20982410.15574595X-RAY DIFFRACTION95.16
1.57-1.60.1882390.14444551X-RAY DIFFRACTION95.21
1.6-1.630.18352400.13344577X-RAY DIFFRACTION94.88
1.63-1.660.18422280.13134335X-RAY DIFFRACTION89.45
1.66-1.70.17842410.12054572X-RAY DIFFRACTION95.78
1.7-1.740.18882420.11964616X-RAY DIFFRACTION96.2
1.74-1.780.17472460.12524664X-RAY DIFFRACTION96.62
1.78-1.830.16862460.13014689X-RAY DIFFRACTION96.9
1.83-1.890.16692450.14044650X-RAY DIFFRACTION96.99
1.89-1.950.18442460.14324699X-RAY DIFFRACTION97.09
1.95-2.020.17182450.13494647X-RAY DIFFRACTION97.04
2.02-2.10.1662480.13284708X-RAY DIFFRACTION97.27
2.1-2.190.17782450.1314665X-RAY DIFFRACTION96.9
2.19-2.310.14992320.13114404X-RAY DIFFRACTION90.9
2.31-2.450.16572480.13494707X-RAY DIFFRACTION97.1
2.45-2.640.15962510.14434764X-RAY DIFFRACTION98.28
2.64-2.910.16692500.14584765X-RAY DIFFRACTION98.33
2.91-3.330.15492530.14914793X-RAY DIFFRACTION98.27
3.33-4.190.13052490.13174740X-RAY DIFFRACTION96.61
4.19-48.620.14672530.15524792X-RAY DIFFRACTION95.68

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