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- PDB-8rah: Crystal structure of class Ie ribonucleotide reductase R2 subunit... -

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Basic information

Entry
Database: PDB / ID: 8rah
TitleCrystal structure of class Ie ribonucleotide reductase R2 subunit with post-translational modification of Y150 into a DOPA from Gardnerella vaginalis
Componentsribonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase R2e / Class Ie RNR / ferritin-like superfamily / NrdF / RNR beta-subunit
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / 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
Similarity search - Component
Biological speciesGardnerella vaginalis ATCC 14019 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJohn, J. / Hogbom, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2021-03992 Sweden
Knut and Alice Wallenberg Foundation2019.0436 Sweden
CitationJournal: Commun Biol / Year: 2025
Title: Characterization of a second class Ie ribonucleotide reductase.
Authors: John, J. / Lundin, D. / Branca, R.M. / Kumar, R. / Srinivas, V. / Lebrette, H. / Hogbom, M.
History
DepositionDec 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Sep 17, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / entity_poly / pdbx_struct_mod_residue / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ribonucleoside-diphosphate reductase
B: ribonucleoside-diphosphate reductase
C: ribonucleoside-diphosphate reductase
D: ribonucleoside-diphosphate reductase


Theoretical massNumber of molelcules
Total (without water)171,3794
Polymers171,3794
Non-polymers00
Water13,583754
1
A: ribonucleoside-diphosphate reductase
C: ribonucleoside-diphosphate reductase


Theoretical massNumber of molelcules
Total (without water)85,6892
Polymers85,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-59 kcal/mol
Surface area24140 Å2
2
B: ribonucleoside-diphosphate reductase
D: ribonucleoside-diphosphate reductase


Theoretical massNumber of molelcules
Total (without water)85,6892
Polymers85,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-57 kcal/mol
Surface area24120 Å2
Unit cell
Length a, b, c (Å)173.710, 173.710, 157.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein
ribonucleoside-diphosphate reductase


Mass: 42844.707 Da / Num. of mol.: 4 / Mutation: Y151DAH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gardnerella vaginalis ATCC 14019 (bacteria)
Gene: HMPREF0421_21333 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E3D8A3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.09 Å3/Da / Density % sol: 69.9 % / Description: transparent rhombohedron
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus G4 condition (0.1 M Carboxylic acids, 0.1 M Buffer System 1 pH 6.5, 37.5% v/v Precipitant Mix 4) + 4% tert-butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97622 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.9→49.68 Å / Num. obs: 215066 / % possible obs: 99.63 % / Redundancy: 16.9 % / Biso Wilson estimate: 45.56 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1316 / Rpim(I) all: 0.03279 / Rrim(I) all: 0.1357 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 13.7 % / Rmerge(I) obs: 4.584 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 21342 / CC1/2: 0.271 / CC star: 0.653 / Rpim(I) all: 1.275 / Rrim(I) all: 4.761 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.68 Å / SU ML: 0.2844 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 1839 0.86 %
Rwork0.171 212458 -
obs0.1712 214297 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.91 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10562 0 0 754 11316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006910950
X-RAY DIFFRACTIONf_angle_d0.758514875
X-RAY DIFFRACTIONf_chiral_restr0.04661631
X-RAY DIFFRACTIONf_plane_restr0.00821921
X-RAY DIFFRACTIONf_dihedral_angle_d13.09924085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.43671360.40515586X-RAY DIFFRACTION95.62
1.95-2.010.31881420.336116252X-RAY DIFFRACTION99.92
2.01-2.070.31781420.281316271X-RAY DIFFRACTION99.95
2.07-2.150.21861370.247416288X-RAY DIFFRACTION99.98
2.15-2.230.25851410.230916310X-RAY DIFFRACTION99.98
2.23-2.340.22941370.190916288X-RAY DIFFRACTION99.98
2.34-2.460.191420.174416339X-RAY DIFFRACTION99.99
2.46-2.610.20371400.170516421X-RAY DIFFRACTION99.98
2.61-2.810.19511420.177116353X-RAY DIFFRACTION100
2.81-3.10.17811430.183416450X-RAY DIFFRACTION100
3.1-3.550.19771420.167316448X-RAY DIFFRACTION100
3.55-4.470.15531450.140716537X-RAY DIFFRACTION100
4.47-49.680.17031500.147316915X-RAY DIFFRACTION99.91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

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)
11.11720780128-0.4955081580790.345522083652.27467237226-0.1086303446171.79816146263-0.05007386133460.216695546606-0.181835566248-0.249603649775-0.0363558402230.2054758255950.173318509729-0.1175125702270.07036089416940.554903661402-0.1188339335430.01835969946720.378038422898-0.02636590098660.42946908635775.523-29.945-84.06
21.225663469020.6677023218261.895684675462.368915855321.347761077766.89180850607-0.00708993898855-0.0776681888704-0.012931933050.2012309528440.00617385808642-0.0374019717716-0.140236062465-0.0141484293821-0.01151243952860.363282816740.003183642244950.09737129579040.2738638722090.005028067494160.32852126273882.514-20.511-51.898
30.6454255815520.2603992809390.4830677719110.9318424946340.1120616552781.88128986149-0.07900974606650.00108420789799-0.0562036656630.1341390296070.06966640868190.035763972496-0.02767598738280.04938677046420.009285735741130.4853031569770.000664813786410.06827413814360.35572953342-0.003177656535530.42780191949683.088-26.889-54.422
40.925405382430.5682612800170.3976869651732.02836724350.5108023719341.87852120795-0.0431828005107-0.0407430510975-0.0400742273190.144749253316-0.01108200812830.248820222371-0.00117241391437-0.2530807475510.04872576366850.444719657230.01296659587460.09175481869610.410025856852-0.01081789597370.44030204966669.067-26.594-54.225
53.765482527382.182417010013.72372394252.650924333372.789557908616.318921785260.0864451459486-0.6440938339670.1388463820640.536572640117-0.1574695080220.3709654710150.133061599825-0.6806389685930.1350776019930.5877802273030.04137875290070.1727111578440.560311538077-0.03315546036840.52281000607364.316-22.475-44.019
61.533436775681.03444388814-0.08389848958042.724901895410.1939269445942.04667644265-0.2109813133420.523746811541-0.0440015179294-0.2744634631720.210200306733-0.204201345022-0.1530256537010.378685540134-0.01650406627610.444029433172-0.1983725358110.0272690077810.710437293846-0.01390442573080.41000954373870.837-63.867-111.105
73.146400313380.940008301252-3.075398726120.9878002696860.2191447765296.917908370030.0989480621124-0.1606891369240.02665926295440.118519234361-0.09720082935780.0487423501-0.002559617070260.0354154415957-0.0041973361530.397395597304-0.0527470002212-0.02877228278610.3313278799130.04629440581040.39028619964559.16-65.265-78.782
81.169046981710.332395725493-0.05467698444670.773971127130.425217689621.009893239360.0533835293213-0.02591373364670.04574160880280.0789433186692-0.0175774291087-0.04456763272410.0385851957502-0.0469152021974-0.03257981191460.46771085791-0.0984658742652-0.003608531693320.4199452900840.01688813675720.43715318461963.202-60.295-81.07
92.453613029510.777180538404-0.872527704020.766983397896-0.2173529983792.271700730120.0331285824927-0.104573003562-0.1740058212680.128744095699-0.0599037318633-0.1108087302570.1954789747760.04813083178350.02920685716350.46752204659-0.0354194072857-0.03700852508390.3409358175480.03550459058220.41780815558873.097-70.728-81.052
107.56690590704-0.336941514633-5.730207511092.8537256823-1.08432873147.673571354310.0202347177766-0.884246659604-0.4853821747750.480618560240.0558363189589-0.01212057325160.3601082764730.384727547501-0.04339060206840.570837647169-0.079343904637-0.0910386454930.4695750201950.1166194761890.46260135692673.14-76.899-70.654
110.929420775892-0.2206768049030.6135960909251.092432898520.4753893947982.11688538380.00279531656484-0.0887659775752-0.1753998919590.100521141709-0.01211895259580.01239035548050.2033694707190.0693690831183-0.008453947547070.4697983338180.002628125281930.0520697406510.3200444324-0.02754423988810.39620251967586.84-34.765-55.837
120.772076364961-0.506650188970.904547628813.18524658141-1.970245758984.25136181508-0.06039189633870.0980715970265-0.0030061589373-0.4181716845610.03048322074380.07318160215250.07859196131640.06638557588220.02735664541930.471142670984-0.0862104284690.04634306027680.349160156219-0.03904191744080.34831633177683.15-16.181-84.032
130.245199929199-0.01450477967910.03378393890371.05236499499-0.4873773411961.76726825036-0.08027421247370.07821597388-0.0644051288713-0.2497177379240.06826701230560.150822216781-0.0335811824693-0.05214900930620.00785487068510.583024851919-0.08631891378090.026840305450.410731121597-0.05012752673840.43226468832180.993-22.706-83.273
140.695684026541-0.9415016515290.3923692927063.34631786371-0.9357994929381.87816983031-0.06254557187450.01117262067250.00491613284836-0.1397347855210.0838971650418-0.0342516197154-0.134379179360.265537962735-0.009929330947910.487626260509-0.09772587842530.06955281346060.428990366664-0.04757724395150.36987810304693.813-20.993-81.633
153.65477164497-3.247340659924.592944530245.19201733704-5.251848911269.671155752320.1887332908060.297322197449-0.164252314204-0.550031720005-0.229286852715-0.219630348110.5310853074260.6076691281440.01828731906720.629302523908-0.053375124520.1359611777630.491687554016-0.09608768814730.41052461646596.874-35.295-88.23
163.74491194447-3.979481132662.391945057995.99855413102-4.101922164123.781778438440.2834794036190.6062205808240.35610156291-0.78746140484-0.357689862714-0.5461190435480.2566089921870.7470566927270.07393324952190.703749965172-0.1375184503960.1795810912730.628011138104-0.03599431530440.471281024643100.391-20.085-93.003
171.337534966840.428504013683-0.6237581143821.277248161640.5113052910531.651888089350.0340822374859-0.1351702141330.2409860613640.0778689383145-0.0209446452177-0.0879140141735-0.1154814513220.0136120910809-0.02855990518420.430711085917-0.07412734995550.01948747513590.3604475476060.04092321343970.42505855461566.703-52.222-82.489
182.035887121791.819500613721.034530958943.377880005872.717678201954.86779814328-0.2637548355050.354064901312-0.0885406998689-0.3324579907420.170745737224-0.0642889393832-0.1814543575950.07477084979670.08629537570580.374224122438-0.0867102323610.01498000933780.5080829818880.03731329020070.35627945501955.854-67.995-110.919
191.282568743920.6413563909710.1353174696741.03606232670.495106303111.26223368622-0.2430786615680.448881765395-0.0791595367944-0.2404640915230.256038996907-0.0559516833108-0.05366824639260.189882534969-0.04004519949970.481327006639-0.145892944910.0369394977020.6147689759460.02894090498880.38287784998862.001-64.913-110.181
201.562977978771.352771020070.3730495746051.56606768310.570914465281.61336834954-0.1835290482670.2649706827990.155302130041-0.1796018541070.0905122809520.0966332656945-0.269082668891-0.1000694595560.07539946508090.505832810172-0.077343164169-0.02699575964430.5499316532950.08558162111120.42063167830951.986-56.855-108.536
211.714573492070.9377323216090.255225868727.926659895476.096015479847.14728641217-0.2995314742130.434517444620.38549123584-1.06396934680.184070845116-0.149927847234-1.199418972550.1779099790990.109294692460.750722158793-0.216410877235-0.1118864598230.631382310940.2059995990170.49738607912959.628-44.718-115.262
222.352338679651.672945913841.201705503487.221264013314.357777810245.34674495779-0.3902389994780.5915283031140.259794572053-1.122007206060.1151114051940.539519163837-0.90390355897-0.2977760479950.264652499220.678644717458-0.101771305337-0.1405768833470.6807988131130.1477301970060.47368310112846.529-53.194-120.094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:73 )A8 - 73
2X-RAY DIFFRACTION2( CHAIN A AND RESID 74:129 )A74 - 129
3X-RAY DIFFRACTION3( CHAIN A AND RESID 130:188 )A130 - 188
4X-RAY DIFFRACTION4( CHAIN A AND RESID 189:285 )A189 - 285
5X-RAY DIFFRACTION5( CHAIN A AND RESID 286:332 )A286 - 332
6X-RAY DIFFRACTION6( CHAIN B AND RESID 8:73 )B8 - 73
7X-RAY DIFFRACTION7( CHAIN B AND RESID 74:129 )B74 - 129
8X-RAY DIFFRACTION8( CHAIN B AND RESID 130:188 )B130 - 188
9X-RAY DIFFRACTION9( CHAIN B AND RESID 189:285 )B189 - 285
10X-RAY DIFFRACTION10( CHAIN B AND RESID 286:332 )B286 - 332
11X-RAY DIFFRACTION11( CHAIN C AND RESID 8:73 )C8 - 73
12X-RAY DIFFRACTION12( CHAIN C AND RESID 74:129 )C74 - 129
13X-RAY DIFFRACTION13( CHAIN C AND RESID 130:188 )C130 - 188
14X-RAY DIFFRACTION14( CHAIN C AND RESID 189:254 )C189 - 254
15X-RAY DIFFRACTION15( CHAIN C AND RESID 255:285 )C255 - 285
16X-RAY DIFFRACTION16( CHAIN C AND RESID 286:332 )C286 - 332
17X-RAY DIFFRACTION17( CHAIN D AND RESID 8:73 )D8 - 73
18X-RAY DIFFRACTION18( CHAIN D AND RESID 74:129 )D74 - 129
19X-RAY DIFFRACTION19( CHAIN D AND RESID 130:188 )D130 - 188
20X-RAY DIFFRACTION20( CHAIN D AND RESID 189:254 )D189 - 254
21X-RAY DIFFRACTION21( CHAIN D AND RESID 255:285 )D255 - 285
22X-RAY DIFFRACTION22( CHAIN D AND RESID 286:332 )D286 - 332

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