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- PDB-9sjy: Serial electron diffraction (SerialED) structure of Ribonucleotid... -

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Basic information

Entry
Database: PDB / ID: 9sjy
TitleSerial electron diffraction (SerialED) structure of Ribonucleotide reductase R2 from E. coli in its oxidised (met) form
ComponentsRibonucleoside-diphosphate reductase 1 subunit beta
KeywordsOXIDOREDUCTASE / serial electron diffraction / SerialED / microcrystal / metalloenzyme / iron / ribonucleotide reductase / electrostatic potential
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)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 1.8 Å
AuthorsPacoste, L. / Kumar, R. / Hongyi, X. / Hofer, G. / Hogbom, M. / Zou, X.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2019-00815 Sweden
Swedish Research Council2021-03992 Sweden
Knut and Alice Wallenberg Foundation2018.0237 Sweden
Knut and Alice Wallenberg Foundation2023.0201 Sweden
CitationJournal: To Be Published
Title: Serial electron diffraction (SerialED) structure of Ribonucleotide reductase R2 from E. coli in its oxidised (met) form
Authors: Pacoste, L.
History
DepositionSep 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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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)87,0776
Polymers86,8542
Non-polymers2234
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-82 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.950, 76.540, 145.740
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: 43426.863 Da / Num. of mol.: 2
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.: 308 / 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: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Ribonucleotide reductase R2 from E. coli in its oxidised (met) form
Type: COMPLEX
Details: Ribonucleotide reductase R2 from E. coli in its oxidised (met) form complexed with irons
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.08938 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 5.5
Details: Crystallization was performed using 23.5 uL protein solution, 25 mM HEPES-Na pH 7.0, 50 mM NaCl, and 20 uL crystallization buffer with seeds, 25 percent PEG 3350, 0.1 M Bis-Tris, pH 5.5.
Buffer component
IDConc.NameFormulaBuffer-ID
125 %PEG 3350H(OCH2CH2)nOH1
20.1 MBis-TrisC8H19NO51
SpecimenConc.: 60 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 55-60 mgmL-1 protein in buffer containing 25 mM HEPES-Na pH 7.0, 50 mM NaCl
Specimen supportDetails: Before applying the sample, the grid was made hydrophilic by immersion in 1% Tween solution followed by blotting.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE
Details: Excess liquid was manually blotted from the backside for approximately 10 seconds, followed by plunge freezing in liquid ethane.

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: To address the preferred orientation of ribbon-shaped crystals on the grid, SerialED data was collected at tilt angles of 0, 10, 25, 45, and 60 degrees. Lower tilts minimized absorption for ...Details: To address the preferred orientation of ribbon-shaped crystals on the grid, SerialED data was collected at tilt angles of 0, 10, 25, 45, and 60 degrees. Lower tilts minimized absorption for improved resolution, while higher tilts expanded reciprocal space coverage.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1 nm / Nominal defocus min: 0 nm / C2 aperture diameter: 20 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 98 K / Temperature (min): 78 K
Image recordingElectron dose: 1.38 e/Å2 / Film or detector model: OTHER / Num. of diffraction images: 6884 / Details: Ceta-D CMOS detector
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
3.99-19.931193.85129.9689516.42
1.8-1.862184.9440.66575142.3
EM diffraction statsDetails: Rsplit is given instead of Rmerge / Fourier space coverage: 88.59 % / High resolution: 1.8 Å / Num. of intensities measured: 4208697 / Num. of structure factors: 68529 / Phase error rejection criteria: 0 / Rmerge: 17.9
ReflectionBiso Wilson estimate: 19.29 Å2

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Processing

EM software
IDNameVersionCategory
6PHENIX1.20.1-4487model fitting
8PHENIXmolecular replacement
12PHENIX3D reconstruction
13PHENIX1.20.1-4487model refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 73.95 Å / B: 76.54 Å / C: 145.74 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 1.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 24.87 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: Maximum-likelihood
Atomic model buildingPDB-ID: 9SJW

9sjw


Accession code: 9SJW / Details: metR2-M / Source name: PDB / Type: experimental model
RefinementResolution: 1.8→19.93 Å / SU ML: 0.247 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.283
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253 1599 2.34 %
Rwork0.2104 66603 -
obs0.2114 68202 88.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.87 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00655884
ELECTRON CRYSTALLOGRAPHYf_angle_d0.95188008
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0498876
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.01251042
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d5.2787783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.37771350.31995616ELECTRON CRYSTALLOGRAPHY82.95
1.86-1.920.38831270.29775741ELECTRON CRYSTALLOGRAPHY84.79
1.92-20.33541470.27485882ELECTRON CRYSTALLOGRAPHY86.5
2-2.090.29371420.24645883ELECTRON CRYSTALLOGRAPHY86.68
2.09-2.20.29751470.23345931ELECTRON CRYSTALLOGRAPHY87.37
2.2-2.340.2541410.22075983ELECTRON CRYSTALLOGRAPHY87.85
2.34-2.520.26981490.20866062ELECTRON CRYSTALLOGRAPHY88.82
2.52-2.770.24621420.21136159ELECTRON CRYSTALLOGRAPHY89.45
2.77-3.170.23241490.20776224ELECTRON CRYSTALLOGRAPHY90.41
3.17-3.990.23921570.17996390ELECTRON CRYSTALLOGRAPHY91.91
3.99-19.930.19961630.17826732ELECTRON CRYSTALLOGRAPHY93.62
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON CRYSTALLOGRAPHY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.47807542331.278134702910.9462701471181.826336621380.8081063923931.050559068760.0322942591962-0.003823935748680.03626474399510.06969925977-0.00485128893119-0.093339795160.0359548112620.0100364599004-0.01903754609980.06487481874230.01835878159580.009923972008120.0838976181577-0.01097383662330.16281754401823.5008363957-1.38013828895-14.5207902841
20.9440251567310.2063593939350.8285024400560.4516792915310.5269506534741.50588357535-0.003733183248520.1481392077410.175303502935-0.1045295682890.00870670344343-0.145338594655-0.1935195450580.1264520263120.009816710487210.1408773978910.007182118898910.030952199730.1325899045660.04799640575280.32715470013422.81409515477.93308705073-29.2685383575
30.916430156680.3451473877860.3525301909380.9124089918570.6473473061111.51854460483-0.004849064939170.1049363074460.103119455731-0.05022096850370.0896553883298-0.0844444374982-0.1211637636970.107860507113-0.09612705255660.08960791870690.00930176502192-0.01309648785450.1256010305370.0009551370370530.25829227202640.19446058551.09363247386-20.0244688348
41.047510738990.100974948485-0.3070696160251.88998385004-0.7679292951431.282590368750.0305088944513-0.04043179391580.3019575344510.06312597726410.0442790849672-0.10051126425-0.159251779116-0.058026089663-0.07390826609880.09482754082780.0089575029332-0.007133856530860.106227274878-0.03329326438580.27886380358614.445701502512.8436971511-11.3825172444
51.087077752830.241479145903-0.1110464485021.28713029250.07824983782290.9333235707180.02573279343940.0537626382071-0.1424993459450.00531896947509-0.08938129777960.0970384063270.16662806347-0.04202649756680.05613710509720.1010205134780.00613073808774-0.005784656633160.105109834762-0.03251768947420.2249518898225.5227862561-14.7065260276-12.7379040905
60.1286696951690.0825078670591-0.4418493026190.692225537733-0.9035643296092.15727943868-0.006244130099790.02534367861220.119385851434-0.0358487224291-0.001495064098380.14734276003-0.0888050644783-0.1803688799150.01865771406590.109702678740.0218374265152-0.03129834800530.1462031983250.007445878262570.304459659047-0.009014279886637.41410529211-27.214072678
70.321355121677-0.1789080419870.1932756786672.44148020535-0.550484972410.987995425324-0.0296557391086-0.03633355457120.2481482824030.02865122140490.000188194885884-0.08209120111630.0782880723343-0.05599877239840.03717803940180.08775668695-0.0128156725570.02069077455050.110303559633-0.003727520787590.17943780927-0.0866705479941-9.05720967448-3.78743563647
83.869608476790.508927985118-0.009145008254651.369104827440.1329492798111.34870927928-0.1710765336030.2772990555990.24033691955-0.3117135583860.192868026610.259046045508-0.0110883229215-0.0581508033308-0.04076937461240.1012437057390.00169469762821-0.02501205332010.284888842634-0.04803844648840.287882172485-10.5157710851.92355813943-15.5241779881
92.735183784910.1708414102070.1516541042663.84593318437-0.3596185880153.28125579838-0.123518399574-0.0338721478441-0.4323882853870.0874336618632-0.0480906699768-0.1126650247270.573191104513-0.1581577776970.03303275466240.105005491666-0.03259854317740.0337296769260.161316389284-0.07905873233590.294936439589-13.670215424-10.8314421803-4.81289930303
100.984977210397-0.992377274321-0.3064067206134.36520795207-2.261174603942.19097943488-0.275777153634-0.31940928472-0.07237468812820.2296792763290.2844025563090.0140553112885-0.0727981363328-0.3432048352840.04792600664320.102384540144-0.0128595521214-0.01370930191640.204064253147-0.06474774338070.300569450789-11.622591054-6.547238968850.345500259306
Refinement TLS group

Refine-ID: ELECTRON CRYSTALLOGRAPHY

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 128 )AA1 - 1281 - 128
22chain 'A' and (resid 129 through 205 )AA129 - 205129 - 205
33chain 'A' and (resid 206 through 341 )AA206 - 341206 - 341
44chain 'B' and (resid 1 through 46 )BB1 - 461 - 46
55chain 'B' and (resid 47 through 152 )BB47 - 15247 - 152
66chain 'B' and (resid 153 through 205 )BB153 - 205153 - 205
77chain 'B' and (resid 206 through 253 )BB206 - 253206 - 253
88chain 'B' and (resid 254 through 291 )BB254 - 291254 - 291
99chain 'B' and (resid 292 through 319 )BB292 - 319292 - 319
1010chain 'B' and (resid 320 through 340 )BB320 - 340320 - 340

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