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- PDB-7z3d: XFEL structure of Class Ib ribonucleotide reductase dimanganese(I... -

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Basic information

Entry
Database: PDB / ID: 7z3d
TitleXFEL structure of Class Ib ribonucleotide reductase dimanganese(II) NrdF in complex with oxidized 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 / membrane / metal ion binding
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 small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like ...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 small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Flavoprotein-like superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / : / 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 Foundation2019.0275 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)51,1766
Polymers50,5922
Non-polymers5844
Water2,864159
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)102,35312
Polymers101,1844
Non-polymers1,1688
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)61.438, 125.634, 144.997
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-549-

HOH

21B-302-

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, 163 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-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
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.82 Å3/Da / Density % sol: 56.4 % / 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 9, 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→51.59 Å / Num. obs: 38319 / % possible obs: 99.91 % / Redundancy: 66.94 % / Biso Wilson estimate: 35.45 Å2 / CC1/2: 0.989 / R split: 0.111 / Net I/σ(I): 3.247
Reflection shellResolution: 2→2.034 Å / Redundancy: 25.42 % / Mean I/σ(I) obs: 0.654 / Num. unique obs: 1881 / CC1/2: 0.32 / R split: 0.863 / % possible all: 100
Serial crystallography measurementCollection time total: 0.5 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 deliveryDescription: drop on tape combined with acoustic droplet ejection
Method: injection
Serial crystallography sample delivery injectionCarrier solvent: mother liquor / Description: acoustic droplet injection / Flow rate: 8 µL/min / Injector temperature: 298 K / Power by: focused acoustic pulse
Serial crystallography data reductionLattices indexed: 14357 / XFEL run numbers: 56-61

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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→24.17 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 1909 4.99 %
Rwork0.1591 36344 -
obs0.1609 38253 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.31 Å2 / Biso mean: 47.4506 Å2 / Biso min: 21.37 Å2
Refinement stepCycle: final / Resolution: 2→24.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3355 0 34 159 3548
Biso mean--34.52 50.78 -
Num. residues----415
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.33341400.31952532267299
2.05-2.110.31231540.259425312685100
2.11-2.170.26711450.239825512696100
2.17-2.240.25021420.215625742716100
2.24-2.320.23361300.193925682698100
2.32-2.410.23831270.177725962723100
2.41-2.520.21691340.174925592693100
2.52-2.650.19971220.167626072729100
2.65-2.820.21621350.168325992734100
2.82-3.040.22161340.171626082742100
3.04-3.340.20291330.153325962729100
3.34-3.820.15061310.133226252756100
3.82-4.810.14651150.118426662781100
4.81-24.170.17841670.145627322899100

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