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- PDB-8bt3: Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, cata... -

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Basic information

Entry
Database: PDB / ID: 8bt3
TitleRibonucleotide Reductase class Ie R2 from Mesoplasma florum, catalytically active radical state solved by XFEL
ComponentsRibonucleoside-diphosphate reductase beta chain
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLebrette, H. / Srinivas, V. / Hogbom, M.
Funding support Sweden, European Union, United States, United Kingdom, 11items
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133081 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM055302 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
Wellcome Trust210734/Z/18/Z United Kingdom
Royal SocietyRSWF/R2/182017 United Kingdom
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 beta chain


Theoretical massNumber of molelcules
Total (without water)39,8451
Polymers39,8451
Non-polymers00
Water2,414134
1
A: Ribonucleoside-diphosphate reductase beta chain

A: Ribonucleoside-diphosphate reductase beta chain


Theoretical massNumber of molelcules
Total (without water)79,6892
Polymers79,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5370 Å2
ΔGint-39 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.985, 46.309, 58.514
Angle α, β, γ (deg.)90.000, 112.590, 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-410-

HOH

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Components

#1: Protein Ribonucleoside-diphosphate reductase beta chain


Mass: 39844.609 Da / Num. of mol.: 1
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 294 K / Method: batch mode
Details: 50 mM calcium acetate, 20 mM ammonium sulphate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.30177 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Dec 10, 2018 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30177 Å / Relative weight: 1
ReflectionResolution: 1.5→66.01 Å / Num. obs: 56800 / % possible obs: 99.97 % / Redundancy: 49.2 % / Biso Wilson estimate: 20.48 Å2 / CC1/2: 0.931 / R split: 0.237 / Net I/σ(I): 52.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 19.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2710 / CC1/2: 0.344 / R split: 0.96 / % possible all: 100
Serial crystallography measurementCollection time total: 0.6 hours / Pulse duration: 35 fsec. / Pulse energy: 2.5 µJ / Pulse photon energy: 9.5 keV
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: Drop on Tape / Flow rate: 9 µL/min

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Processing

Software
NameVersionClassification
cctbx.xfeldata reduction
DIALSdata reduction
cxi.mergedata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→23.82 Å / SU ML: 0.1756 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2137 2841 5.01 %
Rwork0.1775 53906 -
obs0.1793 56747 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.84 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 134 2652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562650
X-RAY DIFFRACTIONf_angle_d0.75293609
X-RAY DIFFRACTIONf_chiral_restr0.0459392
X-RAY DIFFRACTIONf_plane_restr0.005465
X-RAY DIFFRACTIONf_dihedral_angle_d21.3506980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.35671430.32682625X-RAY DIFFRACTION99.53
1.53-1.550.31141320.29712692X-RAY DIFFRACTION99.82
1.55-1.580.351510.2732664X-RAY DIFFRACTION99.82
1.58-1.620.32951390.25382642X-RAY DIFFRACTION99.96
1.62-1.650.30661340.22182735X-RAY DIFFRACTION99.86
1.65-1.690.22761430.20522661X-RAY DIFFRACTION99.79
1.69-1.730.25181380.19092686X-RAY DIFFRACTION99.86
1.73-1.780.23321430.18392705X-RAY DIFFRACTION99.86
1.78-1.830.24641370.17982678X-RAY DIFFRACTION99.86
1.83-1.890.22391430.17932675X-RAY DIFFRACTION99.93
1.89-1.960.23531440.17592700X-RAY DIFFRACTION99.93
1.96-2.040.22841450.16472661X-RAY DIFFRACTION99.96
2.04-2.130.19521380.15162702X-RAY DIFFRACTION100
2.13-2.240.20241390.15152701X-RAY DIFFRACTION99.96
2.24-2.380.18621470.15662692X-RAY DIFFRACTION100
2.38-2.560.20681420.17112724X-RAY DIFFRACTION100
2.56-2.820.19071450.17972684X-RAY DIFFRACTION100
2.82-3.230.18871460.17652738X-RAY DIFFRACTION100
3.23-4.060.1891400.15992730X-RAY DIFFRACTION100
4.07-23.820.22321520.18232811X-RAY DIFFRACTION99.97

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