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

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Basic information

Entry
Database: PDB / ID: 9skg
TitleSerial electron diffraction (SerialED) structure of Ribonucleotide reductase R2 from E. coli in its reduced (red) 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 reduced (red) form
Authors: Pacoste, L.
History
DepositionSep 2, 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
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-85 kcal/mol
Surface area24460 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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Fe / Source: (gene. exp.) Escherichia coli (E. coli)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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 reduced (red) form
Type: COMPLEX
Details: Ribonucleotide reductase R2 from E. coli in its reduced (red) form complexed with irons
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.08908 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
EM crystal formationAtmosphere: Anaerobic
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 50 mM sodium dithionite - and 20 uL crystallization buffer containing seeds, 25 percent ...Details: Crystallization was performed using 23.5 uL protein solution - 25 mM HEPES-Na pH 7.0, 50 mM NaCl and 50 mM sodium dithionite - and 20 uL crystallization buffer containing seeds, 25 percent PEG 3350, 0.1 M Bis-Tris pH 5.5 and 2 mM sodium dithioninte.
Buffer component
IDConc.NameFormulaBuffer-ID
125 %PEG 3350H(OCH2CH2)nOH1
20.1 MBis-TrisC8H19NO51
32 mMSodium dithioniteNa2S2O41
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 reduced with 50 mM sodium dithionite
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. Sample was prepared in an inert environment within a glove box.

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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
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: 5210 / Details: Ceta-D CMOS detector
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
3.99-19.931189.5688.6657816.41
1.86-1.82186.228.04589341.2
EM diffraction statsDetails: Rsplit is given instead of Rmerge / Fourier space coverage: 87.12 % / High resolution: 1.8 Å / Num. of intensities measured: 2868103 / Num. of structure factors: 67392 / Phase error rejection criteria: 0 / Rmerge: 19.8
ReflectionBiso Wilson estimate: 20.72 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: 24.7 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: Maximum-likelihood
Atomic model buildingPDB-ID: 9SK1

9sk1


Accession code: 9SK1 / Source name: PDB / Type: experimental model
RefinementResolution: 1.8→19.93 Å / SU ML: 0.2607 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 1574 2.34 %
Rwork0.1997 65630 -
obs0.2008 67204 86.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00895813
ELECTRON CRYSTALLOGRAPHYf_angle_d0.8167900
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0488868
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.02281021
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d5.9732766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.37991390.3175754ELECTRON CRYSTALLOGRAPHY85
1.86-1.920.33411310.30925790ELECTRON CRYSTALLOGRAPHY85.55
1.92-20.32571480.27735855ELECTRON CRYSTALLOGRAPHY86.13
2-2.090.29141430.24465866ELECTRON CRYSTALLOGRAPHY86.45
2.09-2.20.28961450.22255891ELECTRON CRYSTALLOGRAPHY86.76
2.2-2.340.26031360.20655908ELECTRON CRYSTALLOGRAPHY86.71
2.34-2.520.24421410.20265956ELECTRON CRYSTALLOGRAPHY87.19
2.52-2.770.25981380.20936019ELECTRON CRYSTALLOGRAPHY87.41
2.77-3.170.27421480.20296034ELECTRON CRYSTALLOGRAPHY87.7
3.17-3.990.19781490.16686135ELECTRON CRYSTALLOGRAPHY88.22
3.99-19.930.19961560.15616422ELECTRON CRYSTALLOGRAPHY89.31
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)
10.9788957405820.557920152920.8940776519151.826653529951.095140297473.119307914930.02345479706710.0944850938245-0.0320923042965-0.02494021006320.0108267930877-0.2101595188510.1398863694860.0478554816985-0.05714181130640.0882494839364-0.00370726168920.004278372816190.0917926782227-0.001554664658340.13580601811115.1769599674-14.2833673152-23.7386599456
26.038729379185.579122812112.718095630365.240327013422.439479480651.283132050570.534067591291-0.9408282622820.2890260462770.78525229684-0.618088211130.1897335924790.186833738508-0.3897508035340.1172829164770.224736752967-0.00806208397587-0.02588415644270.238992190368-0.03056735463280.27232343875832.59604048497.362129370131.96030139859
35.795476357533.695248491464.693309289163.029977879223.50335156674.16400539677-0.01584781199430.227805005890.213422578320.003969595697060.0512692486929-0.09166553546240.06581735012350.257850897759-0.02380452878130.1249721724820.0110271317661-5.76153105797E-50.1306953620160.0004485662232960.20848789191530.075817639410.065924667-14.6904154564
41.321693649050.5191830366460.6014129970131.860311739961.093711195961.58490845049-0.09910103407070.00824889691240.362531673020.107243505073-0.0149535319450.12917465093-0.05597321622360.09394044754670.07843617669840.08829520629370.00616850778710.002113087373570.1161650514230.0007417579623980.2577003579324.18503149856.27111629573-11.384990099
51.902898179080.2294667633650.449476554241.754794322840.9924735180323.70942593359-0.2051001558590.2094385712560.482526837614-0.2342952210920.108012377255-0.260528889387-0.5081490968380.3600309036480.1246444024560.2052451853880.02052454210940.007036358697190.108834597730.04219150424920.30711312492522.38136748348.73059578137-30.1543119513
63.71703373919-1.309955578052.408302352030.481684699501-0.7511350334253.099441119490.08489566160740.3674791538450.330848863489-0.107317823608-0.171366390782-0.085506391525-0.01538764601660.2056326144110.07138713472790.1482130261160.01855551394960.02387001749770.1396347702590.03529791891350.18487883225221.27806311311.91437209046-37.1874574082
71.28512253185-0.206744879161-1.621378143071.63147494911-0.2693147574552.936062084650.286895961960.106476511937-0.09114333547640.09430413078720.179516284868-0.3083737135470.247103621723-0.380733837056-0.2967563200850.159762103075-0.004549079041-0.06186595226930.134841216967-0.03127129350020.32850178759641.84952600566.19444445724-7.52622061487
81.081641349710.514608321330.304760212141.112321792490.9722061439211.66532754878-0.0279465945710.1564985920210.0218329819559-0.1074654093110.0924877449657-0.191975875935-0.07746799222850.0420291352858-0.05515397848620.1147601115910.02926563787180.01001979064570.140314045664-0.01934950688220.24168025546934.1986928731-1.13601773926-24.6068804257
92.183611357271.320823237431.993827614724.05454971223.10533079063.92938916979-0.0873282295706-0.05067452940790.237939578798-0.00478801101087-0.0290546000752-0.0623778484265-0.08470726518060.05530409432110.123504542750.123336848781-0.02244794958410.04451451823290.232143552118-0.07355140891730.38485778454246.90732447325.59306411072-18.5679629302
100.1474066262350.2967093706330.7013285902490.8302853848141.195063613583.44967423415-0.04248696634630.271953893274-0.511405110793-0.06422772893030.259335033576-0.6056769046760.04829874398040.35898144536-0.2195177974130.141787821383-0.02005506461110.0489238202210.246686586353-0.1092427759560.4352093050647.1103838351-2.41931076734-17.7512653188
110.879477677838-0.2625493499990.07632007506672.07021951448-1.051969078142.17332185338-0.00875239415191-0.01602946121850.2489634551230.01322230222480.1174469396020.116477696634-0.161035910054-0.118016523625-0.144031777990.08985929433030.000965333451519-0.0005196911294940.120150093857-0.037062128530.24769916934814.528417220713.0359487019-11.6083876173
121.513803447670.592688554026-0.2968290883463.34067776489-0.2891330048470.873641681373-0.0106757428662-0.0210796758672-0.2934114185080.00732786252494-0.04525408664180.02926800516520.167506086157-0.07030295333950.04430908837310.1166328412270.00047188025658-0.01327679883420.119117155514-0.01162164103910.1753195980435.93462642343-14.641732968-12.5569942949
130.3262959861750.247746269293-0.6140932384590.986070322172-1.537497009043.471836158070.004812135993150.06779431259010.0844016435019-0.004563387128180.04293138259660.101578251854-0.0414400427981-0.188771881086-0.06548459950310.1060069799240.0267625961174-0.01739802629660.158571885695-0.01268480511690.2244821017960.1033555755677.64330822341-26.9779099468
141.07624026336-0.1523931816230.3774458222494.82631109177-0.3373751267090.4326677246230.0283663441687-0.143399252716-0.08523872247970.238530523056-0.01462186235120.1291850563220.0936454659689-0.119562434206-0.03309828309590.154817277645-0.02420058870650.04357175927810.189666844931-0.01523185448610.1694174611910.528304911968-8.4860889755-3.75821057305
151.823224731240.8232117196220.1444833885450.87854150823-0.6534797444291.10635795676-0.1470798922810.1709474784320.0467403083046-0.2160615287550.1659811304170.03578387974760.0139385367657-0.0559774812450.004662360884810.1187011810970.02288408249590.05125233365950.242342878132-0.05480656741710.141345354469-9.688716679722.79891791701-15.6596573487
162.66592222012-1.51860402701-0.05523024883226.04480269084-1.667479478722.62483349011-0.187937028471-0.297325250246-0.3118352085340.1782209450210.1361688336620.2810329170810.201149306707-0.254442779030.07054411838340.122418352915-0.01642823254870.05332003512020.198370813202-0.01258385212760.215708794879-12.6648803839-9.36744742987-2.86917455603
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 45 )AA1 - 451 - 45
22chain 'A' and (resid 46 through 66 )AA46 - 6646 - 66
33chain 'A' and (resid 67 through 98 )AA67 - 9867 - 98
44chain 'A' and (resid 99 through 143 )AA99 - 14399 - 143
55chain 'A' and (resid 144 through 170 )AA144 - 170144 - 170
66chain 'A' and (resid 171 through 206 )AA171 - 206171 - 206
77chain 'A' and (resid 207 through 224 )AA207 - 224207 - 224
88chain 'A' and (resid 225 through 290 )AA225 - 290225 - 290
99chain 'A' and (resid 291 through 319 )AA291 - 319291 - 319
1010chain 'A' and (resid 320 through 341 )AA320 - 341320 - 341
1111chain 'B' and (resid 1 through 46 )BB1 - 461 - 46
1212chain 'B' and (resid 47 through 152 )BB47 - 15247 - 152
1313chain 'B' and (resid 153 through 206 )BB153 - 206153 - 206
1414chain 'B' and (resid 207 through 253 )BB207 - 253207 - 253
1515chain 'B' and (resid 254 through 290 )BB254 - 290254 - 290
1616chain 'B' and (resid 291 through 340 )BB291 - 340291 - 340

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