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- PDB-7z3e: XFEL structure of Class Ib ribonucleotide reductase dimanganese(I... -

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Basic information

Entry
Database: PDB / ID: 7z3e
TitleXFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with hydroquinone NrdI from Bacillus cereus
Components
  • Protein NrdI
  • Ribonucleoside-diphosphate reductase subunit beta
KeywordsOXIDOREDUCTASE / Ribonucleotide reductase R2b / Class Ib RNR / Flavoprotein / Metalloenzyme / ferritin-like superfamily / dimanganese cofactor / XFEL
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein modification process / FMN binding / metal ion binding / membrane
Similarity search - Function
Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family ...Ribonucleotide reductase, class Ib, NrdI, bacterial / Ribonucleotide reductase Class Ib, NrdI / NrdI Flavodoxin like / Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Flavoprotein-like superfamily / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FNR / : / Protein NrdI / Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJohn, J. / Lebrette, H. / Aurelius, O. / Hogbom, M.
Funding support Sweden, European Union, 5items
OrganizationGrant numberCountry
Swedish Research Council2017-04018 Sweden
Swedish Research Council2021-03992 Sweden
European Research Council (ERC)HIGH-GEAR 724394European Union
Knut and Alice Wallenberg Foundation2017.0275 Sweden
Knut and Alice Wallenberg Foundation2021-03992 Sweden
CitationJournal: Elife / Year: 2022
Title: Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography.
Authors: John, J. / Aurelius, O. / Srinivas, V. / Saura, P. / Kim, I.S. / Bhowmick, A. / Simon, P.S. / Dasgupta, M. / Pham, C. / Gul, S. / Sutherlin, K.D. / Aller, P. / Butryn, A. / Orville, A.M. / ...Authors: John, J. / Aurelius, O. / Srinivas, V. / Saura, P. / Kim, I.S. / Bhowmick, A. / Simon, P.S. / Dasgupta, M. / Pham, C. / Gul, S. / Sutherlin, K.D. / Aller, P. / Butryn, A. / Orville, A.M. / Cheah, M.H. / Owada, S. / Tono, K. / Fuller, F.D. / Batyuk, A. / Brewster, A.S. / Sauter, N.K. / Yachandra, V.K. / Yano, J. / Kaila, V.R.I. / Kern, J. / Lebrette, H. / Hogbom, M.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase subunit beta
B: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1786
Polymers50,5922
Non-polymers5864
Water2,540141
1
A: Ribonucleoside-diphosphate reductase subunit beta
B: Protein NrdI
hetero molecules

A: Ribonucleoside-diphosphate reductase subunit beta
B: Protein NrdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,35712
Polymers101,1844
Non-polymers1,1738
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10710 Å2
ΔGint-78 kcal/mol
Surface area31220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.237, 125.795, 144.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ribonucleoside-diphosphate reductase subunit beta


Mass: 37052.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria)
Strain: ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711
Gene: BC_1355 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q81G55, ribonucleoside-diphosphate reductase
#2: Protein Protein NrdI


Mass: 13539.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria)
Gene: nrdI, A9485_05295, B4082_4779, BKK64_22520, BLD50_28200, BLX06_07420, C1N66_03050, C6A78_17740, C6Y54_16250, CJ306_07140, CN357_26430, CN553_06005, CN980_12615, COD77_14575, COI69_30475, COI98_ ...Gene: nrdI, A9485_05295, B4082_4779, BKK64_22520, BLD50_28200, BLX06_07420, C1N66_03050, C6A78_17740, C6Y54_16250, CJ306_07140, CN357_26430, CN553_06005, CN980_12615, COD77_14575, COI69_30475, COI98_10480, COM79_20950, CON36_20815, CON37_10850, CSW12_06330, D0437_06525, DR116_0000380, DX932_00180, E2F98_13910, F8165_13725, F8172_22390, FC692_08670, FC695_16850, FC702_30940, FORC47_1246, GE376_06770, JDS76_16260, TU58_02775, WR52_06765
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0YPL1

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Non-polymers , 4 types, 145 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.84 % / Description: Yellow rhombohedron shaped crystals
Crystal growTemperature: 293 K / Method: batch mode / pH: 5 / Details: 0.1 M MnCl2, 0.1 M sodium acetate 5.0, 5% PEG 6000

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.300734 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Dec 12, 2018 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.300734 Å / Relative weight: 1
ReflectionResolution: 2→51.47 Å / Num. obs: 38188 / % possible obs: 99.91 % / Redundancy: 59.92 % / Biso Wilson estimate: 33.22 Å2 / CC1/2: 0.988 / R split: 0.111 / Net I/σ(I): 3.28
Reflection shellResolution: 2→2.034 Å / Redundancy: 26.46 % / Mean I/σ(I) obs: 0.791 / Num. unique obs: 1880 / CC1/2: 0.391 / R split: 0.765 / % possible all: 100
Serial crystallography measurementCollection time total: 0.75 hours / Collimation: compound refractive lenses / Pulse duration: 35 fsec. / Pulse energy: 4 µJ / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: mother liquor / Description: acoustic droplet ejection / Injector temperature: 298 K / Power by: focused acoustic pulse
Serial crystallography data reductionLattices indexed: 13509 / XFEL run numbers: 183-191

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
cctbx.xfeldata reduction
PHASERphasing
cctbx.xfel.mergedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bmo

4bmo


Resolution: 2→23.91 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 1897 4.98 %
Rwork0.1516 36222 -
obs0.1532 38119 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.41 Å2 / Biso mean: 43.9762 Å2 / Biso min: 20.5 Å2
Refinement stepCycle: final / Resolution: 2→23.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 34 141 3537
Biso mean--30.37 47.29 -
Num. residues----416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.050.34861380.300325282666
2.05-2.110.2791550.237125402695
2.11-2.170.22941420.213125372679
2.17-2.240.21991430.193125472690
2.24-2.320.2211280.173925942722
2.32-2.410.22211260.165625582684
2.41-2.520.21751370.16325682705
2.52-2.650.18081180.161125982716
2.65-2.820.2241350.168625802715
2.82-3.040.20681320.16326012733
3.04-3.340.17591340.148225862720
3.34-3.820.14021320.128526222754
3.82-4.810.13321130.115726452758
4.81-23.910.16941640.134727182882
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)
14.1272.01610.03268.6817-1.46419.1906-0.12590.432-0.174-1.42690.06970.1549-0.0395-0.0380.01570.36710.0294-0.01330.31230.010.242521.2562-1.9987-17.9859
21.04590.32540.16093.19441.24472.89070.0693-0.11640.01290.2194-0.0538-0.2187-0.13580.2088-0.03680.2209-0.0183-0.01320.19910.05350.240426.481210.60465.2692
35.3773-1.45385.70226.70310.33517.52920.0268-1.317-0.07091.1130.04190.0635-0.042-0.611-0.04640.7873-0.07260.07740.48510.0130.388620.359915.036122.3588
44.32914.05634.48175.90797.04479.05680.2837-0.0042-0.19180.8067-0.2589-0.03110.2714-0.759-0.07550.34120.04720.04380.31090.04430.40957.875414.69444.5404
55.34942.85830.44888.2589-1.46495.3262-0.17550.1599-0.0493-0.47770.21670.237-0.2676-0.2899-0.01580.17640.07320.01910.1953-0.00710.25859.554211.2166-6.0664
64.31521.15012.99462.34771.30494.33480.19640.0194-0.04950.1133-0.0886-0.1544-0.05520.137-0.11090.2793-0.01880.02670.16890.04760.21925.357117.9713-0.9595
77.99223.28736.50465.31193.97488.80520.1233-0.16620.2534-0.0378-0.13340.5798-0.5605-0.56150.08080.33850.08950.06970.22720.04180.37710.181825.6926-0.4231
82.42220.35722.39274.30451.24255.6713-0.25290.20880.5115-0.259-0.04770.105-0.95270.30970.3010.3606-0.00490.01450.2130.05410.326121.211930.0242-3.8606
96.1706-2.4624-1.96828.5095.86484.093-0.0053-0.0676-0.6107-0.19950.4311-1.78950.21650.7457-0.36640.5404-0.07190.01370.42750.04030.625638.673817.3972-1.1344
109.54850.6815-4.88939.4536-3.50753.89330.12190.94280.1377-0.31640.16690.0106-0.4829-1.0528-0.33980.52710.05450.02070.47310.01160.222127.287424.7297-24.1729
119.2859-0.5735-3.39027.68974.31713.9145-0.31060.8364-0.1429-0.43160.0533-0.1854-0.0313-0.18720.27380.80040.0160.10690.64560.10170.313733.257522.4874-33.629
127.64331.025-3.31655.8863-2.17992.6893-0.13590.4848-0.3647-0.64390.0066-0.50910.16960.7530.14660.4281-0.02460.10610.4512-0.01490.31838.59819.1991-24.3565
137.404-0.9685-4.12194.959-0.68467.37410.04130.08080.1416-0.2039-0.009-0.301-0.43740.5929-0.0520.3276-0.0980.02730.3368-0.02220.250338.130524.3963-14.5313
147.92014.5765-3.78553.487-4.15277.77420.23620.72281.6999-0.12970.3477-0.0326-2.01860.0599-0.64421.2507-0.08730.10450.55180.12470.692234.785637.416-21.8042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 13 )A1 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 107 )A14 - 107
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 123 )A108 - 123
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 140 )A124 - 140
5X-RAY DIFFRACTION5chain 'A' and (resid 141 through 162 )A141 - 162
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 214 )A163 - 214
7X-RAY DIFFRACTION7chain 'A' and (resid 215 through 247 )A215 - 247
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 280 )A248 - 280
9X-RAY DIFFRACTION9chain 'A' and (resid 281 through 298 )A281 - 298
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 19 )B1 - 19
11X-RAY DIFFRACTION11chain 'B' and (resid 20 through 35 )B20 - 35
12X-RAY DIFFRACTION12chain 'B' and (resid 36 through 70 )B36 - 70
13X-RAY DIFFRACTION13chain 'B' and (resid 71 through 102 )B71 - 102
14X-RAY DIFFRACTION14chain 'B' and (resid 103 through 118 )B103 - 118

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