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- PDB-9sig: XFEL structure of oxidised Ribonucleotide reductase R2a Y122F mut... -

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Basic information

Entry
Database: PDB / ID: 9sig
TitleXFEL structure of oxidised Ribonucleotide reductase R2a Y122F mutant from E. coli
ComponentsRibonucleoside-diphosphate reductase 1 subunit beta
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase beta subunit / R2a / Di-iron beta subunit / 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: 1.9 Å
AuthorsKumar, R. / Srinivas, V. / Hogbom, M.
Funding support Sweden, United States, 9items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2023.0201 Sweden
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM149528 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM151988 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM154040 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
Department of Energy (DOE, United States)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

Downloads & links

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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
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.960, 76.549, 145.738
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-FE / FE (III) 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.: 249 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 297 K / Method: batch mode / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5, PEG 3350 25% / PH range: 5-6 / 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: 1.26295 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26295 Å / Relative weight: 1
ReflectionResolution: 1.9→36.43 Å / Num. obs: 65872 / % possible obs: 99.94 % / Redundancy: 20 % / Biso Wilson estimate: 22.41 Å2 / CC1/2: 0.98 / Net I/σ(I): 5.831
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 3197 / CC1/2: 0.41
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: 1.9→36.43 Å / SU ML: 0.1757 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.4785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1853 2003 3.04 %
Rwork0.1508 63869 -
obs0.1519 65872 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 4 249 5829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01715746
X-RAY DIFFRACTIONf_angle_d1.34337804
X-RAY DIFFRACTIONf_chiral_restr0.0884864
X-RAY DIFFRACTIONf_plane_restr0.01271003
X-RAY DIFFRACTIONf_dihedral_angle_d17.13082138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30721400.25644452X-RAY DIFFRACTION99.33
1.95-20.27861360.22034524X-RAY DIFFRACTION100
2-2.060.24991480.19754492X-RAY DIFFRACTION100
2.06-2.130.19951390.17184527X-RAY DIFFRACTION99.98
2.13-2.20.20061430.16314494X-RAY DIFFRACTION100
2.2-2.290.20411430.16344496X-RAY DIFFRACTION100
2.29-2.390.19671380.15914571X-RAY DIFFRACTION99.98
2.39-2.520.2311440.164517X-RAY DIFFRACTION99.96
2.52-2.680.19791440.15664540X-RAY DIFFRACTION100
2.68-2.880.19881420.15994576X-RAY DIFFRACTION100
2.88-3.170.18911450.15494582X-RAY DIFFRACTION100
3.17-3.630.17511460.1394613X-RAY DIFFRACTION100
3.63-4.580.12751410.11264644X-RAY DIFFRACTION100
4.58-36.430.14821540.12984841X-RAY DIFFRACTION99.9

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