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- PDB-9sih: XFEL structure of Ribonucleotide reductase R2a Y122F mutant from ... -

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Basic information

Entry
Database: PDB / ID: 9sih
TitleXFEL structure of Ribonucleotide reductase R2a Y122F mutant from E. coli,reduced form
ComponentsRibonucleoside-diphosphate reductase 1 subunit beta
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase beta subunit / R2a / Di-iron beta subunit / Reduced R2a / XFEL structure
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / 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 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKumar, R. / Srinivas, V. / Hogbom, M.
Funding support Sweden, United States, 3items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2023.0201 Sweden
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM149528; GM110501; GM126289; GM117126; GM151988; R24GM154040 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515; DE-AC02-05CH11231 United States
CitationJournal: Structure / Year: 2026
Title: Tracking the redox reaction of the iron enzyme ribonucleotide reductase using continuous SerialED and SFX.
Authors: Pacoste, L. / Kumar, R. / Srinivas, V. / Makita, H. / Simon, P.S. / Bannerjee, R. / Minnetian, N.M. / Bhowmick, A. / Paley, D.W. / Mittan-Moreau, D.W. / Chatterjee, K. / Rosenberg, D.J. / ...Authors: Pacoste, L. / Kumar, R. / Srinivas, V. / Makita, H. / Simon, P.S. / Bannerjee, R. / Minnetian, N.M. / Bhowmick, A. / Paley, D.W. / Mittan-Moreau, D.W. / Chatterjee, K. / Rosenberg, D.J. / Batyuk, A. / Gee, L.B. / Alonso-Mori, R. / Sauter, N.K. / Yano, J. / Yachandra, V.K. / John, J. / Aurelius, O. / Brewster, A.S. / Kern, J.F. / Blomberg, B. / Lebrette, H. / Xu, H. / Hofer, G. / Hogbom, M. / Zou, X.
History
DepositionAug 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.1May 20, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 17, 2026Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase 1 subunit beta
B: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0456
Polymers86,8222
Non-polymers2234
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-81 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.182, 76.446, 146.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ribonucleoside-diphosphate reductase 1 subunit beta / Protein B2 / Protein R2 / Ribonucleotide reductase 1


Mass: 43410.863 Da / Num. of mol.: 2 / Mutation: Y122F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nrdB, ftsB, b2235, JW2229
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 297 K / Method: batch mode / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5, PEG 3350 25% / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.27824 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Feb 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27824 Å / Relative weight: 1
ReflectionResolution: 1.7→26.42 Å / Num. obs: 92055 / % possible obs: 99.98 % / Redundancy: 62.97 % / Biso Wilson estimate: 19.87 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.51
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 0.945 / Num. unique obs: 6482 / CC1/2: 0.28
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
cctbx.xfeldata reduction
cxi.mergedata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→26.42 Å / SU ML: 0.2356 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.7142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1905 2000 2.17 %
Rwork0.158 90055 -
obs0.1587 92055 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.23 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5577 0 4 362 5943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01675849
X-RAY DIFFRACTIONf_angle_d1.43737960
X-RAY DIFFRACTIONf_chiral_restr0.0874880
X-RAY DIFFRACTIONf_plane_restr0.01481027
X-RAY DIFFRACTIONf_dihedral_angle_d17.36672185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.34211370.31736345X-RAY DIFFRACTION99.92
1.74-1.790.32411470.30016327X-RAY DIFFRACTION99.97
1.79-1.840.31331330.26796376X-RAY DIFFRACTION99.98
1.84-1.90.28181410.24676406X-RAY DIFFRACTION99.98
1.9-1.970.28061440.21936348X-RAY DIFFRACTION100
1.97-2.050.24061410.20086372X-RAY DIFFRACTION99.98
2.05-2.140.22791360.19316374X-RAY DIFFRACTION100
2.14-2.250.20251470.16026430X-RAY DIFFRACTION100
2.25-2.40.21081450.15276410X-RAY DIFFRACTION100
2.4-2.580.18181370.15676422X-RAY DIFFRACTION100
2.58-2.840.1731490.15416456X-RAY DIFFRACTION100
2.84-3.250.19931440.14826480X-RAY DIFFRACTION100
3.25-4.090.14641460.11946550X-RAY DIFFRACTION100
4.09-26.420.13981530.12026759X-RAY DIFFRACTION99.87

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