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- PDB-9sk1: Serial electron diffraction (SerialED) structure of Y122F mutant ... -

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Basic information

Entry
Database: PDB / ID: 9sk1
TitleSerial electron diffraction (SerialED) structure of Y122F mutant 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. / Srinivas, V. / 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 Y122F mutant Ribonucleotide reductase R2 from E. coli in its reduced (red) 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)87,0456
Polymers86,8222
Non-polymers2234
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-84 kcal/mol
Surface area24240 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: 43410.863 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: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: Y122F mutant of Ribonucleotide reductase R2 from E. coli in its reduced (red) form
Type: COMPLEX
Details: Y122F mutant of Ribonucleotide reductase R2 from E. coli in its reduced (red) form complexed with irons
Entity ID: #1 / 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 / 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: 9670 / Details: Ceta-D CMOS detector
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
3.99-19.931185.44299.99627713.36
1.86-1.82182.1774.55563131.52
EM diffraction statsDetails: Rsplit is given instead of Rmerge / Fourier space coverage: 83.1 % / High resolution: 1.8 Å / Num. of intensities measured: 7929116 / Num. of structure factors: 64279 / Phase error rejection criteria: 0 / Rmerge: 13.5
ReflectionBiso Wilson estimate: 21.11 Å2

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Processing

EM software
IDNameVersionCategory
6PHENIX1.20.1-4487model fitting
8PHENIX1.20.1-4487model refinement
9PHENIXmolecular replacement
13PHENIX3D reconstruction
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: 26.54 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: Maximum-likelihood
Atomic model buildingPDB-ID: 1xik

1xik


Accession code: 1xik / Source name: PDB / Type: experimental model
RefinementResolution: 1.8→19.93 Å / SU ML: 0.2265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2105
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 1543 2.41 %
Rwork0.1961 62537 -
obs0.1967 64080 82.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.54 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00436007
ELECTRON CRYSTALLOGRAPHYf_angle_d0.69768171
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0402893
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.02261064
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d6.0899800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.34231380.30455493ELECTRON CRYSTALLOGRAPHY81.22
1.86-1.920.32871290.28365540ELECTRON CRYSTALLOGRAPHY81.91
1.92-20.29231320.25075610ELECTRON CRYSTALLOGRAPHY82.38
2-2.090.24571410.2265598ELECTRON CRYSTALLOGRAPHY82.56
2.09-2.20.2441420.20265609ELECTRON CRYSTALLOGRAPHY82.66
2.2-2.340.24131410.19515614ELECTRON CRYSTALLOGRAPHY82.57
2.34-2.520.22661420.18725642ELECTRON CRYSTALLOGRAPHY82.71
2.52-2.770.23471390.19355703ELECTRON CRYSTALLOGRAPHY82.94
2.77-3.170.23571430.19595734ELECTRON CRYSTALLOGRAPHY83.37
3.17-3.990.17911520.17055861ELECTRON CRYSTALLOGRAPHY84.42
3.99-19.930.1861440.17526133ELECTRON CRYSTALLOGRAPHY85.23
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)
12.453056145081.794508873121.571200137192.26828144751.463994306641.497702748580.03040245396910.01587182003630.04930880638960.03473278363640.00718215200786-0.01737292466450.0351641981346-0.00299474590393-0.0267034830410.07140396292640.02895829998110.03614491722710.113690548143-0.009636191295420.10476005731124.2425162844-1.3942114583-15.0850833884
20.8457478604510.05895393425710.5502762191690.3482456959880.2958841292241.84055954029-0.04822944655390.09125961497170.184759709679-0.13370625816-0.0287804850276-0.0775590092572-0.2608557771150.0371499106660.08412739197320.1371340025190.01806880659110.01872595808860.1529235416980.01583651196640.19823733943522.72840266175.60730968663-24.3327140396
30.4778673190940.3803093210170.1267944374521.345213191090.6243996859080.884436758283-0.02013278360920.11521611873-0.0555325537373-0.118674807780.0577108597842-0.257945324834-0.06383789518350.0769112533805-0.06051121445440.1143109464960.01077960511390.0291858797070.185747989657-0.02143849171710.26244969647936.03639602650.537982150798-21.0042922301
44.637722219622.100600795251.446633446975.863295886742.944678302984.412671182620.0198463767653-0.3009325942450.02536439480840.0207540327391-0.0844842826473-0.214200322473-0.2138449896550.1723301847970.07398323001440.123667909437-0.03780000286580.04613642794130.290862337742-0.07523108991590.28295483226547.25112287636.18730003917-17.8617899331
52.08669130639-0.03947960705742.678375545140.9502366016141.613152598256.340204937170.2179496032960.353805431086-0.305493331024-0.1697321509120.333747959418-0.599059364625-0.08090223387740.522393896957-0.4948110058460.181692891781-0.009651671347870.03918950912650.204305954786-0.08076699332530.4553634091947.5854418887-2.27556561131-18.2118601958
63.85823488717-1.03306388517-1.550660035233.349816963431.156640876372.696754959960.210917436910.1823019429450.684833523353-0.05793373427030.164717653505-0.394633241825-0.124775839051-0.0815040211527-0.2827499995390.1381251659150.0157418982433-0.01540441831920.1164952996010.03245672813130.19543798460415.124985536817.4487652703-18.8258005889
71.293199966230.293220080271-0.04683294350333.40147944719-0.03843092049520.809345763639-0.00166808382375-0.0813670012136-0.02117261550730.153350030436-0.0301358077308-0.07131730075050.1081453146280.0007986523306120.03232210279580.0758926826390.01019165719720.003205288684660.146876190422-0.006866610957950.1045645480599.14215471176-7.5012478276-9.69047867571
84.92855568519-2.652732611780.755552989279.09077512821-2.246705144865.96466865995-0.3059584467290.229038308284-0.662212733081-0.01845869910820.4555940947770.458551473863-0.367986446479-0.673085401705-0.06369153540410.192792198053-0.0066574380499-0.02578266500640.254703343444-0.06080142773250.312795425753-1.97960618243-18.2986774237-21.4309566097
90.3060732909210.221627661453-0.9782748538510.892564556556-1.339833226893.97838134476-0.02043997090380.01551982902150.067220939591-0.06249303205860.02009976574460.135308856114-0.042625721157-0.299906854222-0.05251299676850.08102124203220.0233880930055-0.02821093993250.170420080072-0.00819254950510.2370442256720.02814176952657.17001288292-26.6745788622
103.37390250177-3.561378936292.864022248576.84172205368-4.368951163273.085923169450.0250537931857-0.2338594536760.05753009916440.547828183095-0.1606306983860.284573293761-0.130174633639-0.1365284750610.1229057102150.258693812488-0.09180849670710.07210694710420.310808499641-0.004060708748770.183126325333-3.04196886767-18.0371210126-2.12244225793
113.08761213345-3.056082959591.377849097514.79525998319-2.071343287851.87571237147-0.0549329678139-0.0367348920543-0.034327142740.1933465973560.01611727028520.00289064968307-0.0321364543255-0.07261255177950.04579138288210.0779852994496-0.02971720270.02204025605080.105496398516-0.0426604858660.1194957119842.639843065220.150826137938-5.71520344314
121.96665079407-1.275378968370.8717146976296.29104371445-0.9592764648833.37954254161-0.161731798030.0838805840023-0.375196650893-0.1548920846070.00730940485720.02114195588720.164755756961-0.1364712406430.1737094264890.105927247148-0.006523698219820.0644358464170.196748523305-0.07015091676080.238267496407-10.83488503520.821149253949-16.3394468207
130.982521810037-1.120542640660.4453748115663.88147593522-1.463724085912.28522669059-0.103166973929-0.0443499513782-0.302682830164-0.1300082466790.07642388838040.1008422459970.322994636923-0.2973739469820.06838031769870.150719784453-0.06525244219660.06868628210740.223223283249-0.04366565772220.370601991156-12.6289454362-10.4238900468-3.14361753616
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 98 )AA1 - 981 - 98
22chain 'A' and (resid 99 through 205 )AA99 - 20599 - 205
33chain 'A' and (resid 206 through 290 )AA206 - 290206 - 290
44chain 'A' and (resid 291 through 319 )AA291 - 319291 - 319
55chain 'A' and (resid 320 through 341 )AA320 - 341320 - 341
66chain 'B' and (resid 1 through 19 )BB1 - 191 - 19
77chain 'B' and (resid 20 through 129 )BB20 - 12920 - 129
88chain 'B' and (resid 130 through 152 )BB130 - 152130 - 152
99chain 'B' and (resid 153 through 206 )BB153 - 206153 - 206
1010chain 'B' and (resid 207 through 224 )BB207 - 224207 - 224
1111chain 'B' and (resid 225 through 258 )BB225 - 258225 - 258
1212chain 'B' and (resid 259 through 290 )BB259 - 290259 - 290
1313chain 'B' and (resid 291 through 340 )BB291 - 340291 - 340

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