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- PDB-9d9u: Rhodospirillum rubrum Nitrogenase-like Methylthio-alkane Reductas... -

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Basic information

Entry
Database: PDB / ID: 9d9u
TitleRhodospirillum rubrum Nitrogenase-like Methylthio-alkane Reductase Complex with an Oxidized P-cluster
Components(Nitrogenase) x 2
KeywordsOXIDOREDUCTASE / Methylthio-alkane reductase / Carbon-Sulfur lyase / dimethylsulfide / methane / methanethiol
Function / homology: / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase / nitrogenase / nitrogenase activity / FE(8)-S(7) CLUSTER / Nitrogenase / Nitrogenase
Function and homology information
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsKreitler, D.F. / Hu, G. / North, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)KP1607011 United States
Department of Energy (DOE, United States)DE-SC0022091 United States
Department of Energy (DOE, United States)DE-SC0024125 United States
CitationJournal: Nat Catal / Year: 2025
Title: Architecture, catalysis and regulation of methylthio-alkane reductase for bacterial sulfur acquisition from volatile organic compounds
Authors: Murali, S. / Hu, G.B. / Kreitler, D.F. / Carriedo, A.A. / Lewis, L.C. / Fosu, S.A. / Weaver, O.G. / Buzas, E.M. / Byerly, K.M. / Yoshikuni, Y. / McSweeney, S. / Shafaat, H.S. / North, J.A.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrogenase
B: Nitrogenase
C: Nitrogenase
D: Nitrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,2816
Polymers216,9394
Non-polymers1,3422
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Nitrogenase


Mass: 57613.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Gene: Rru_A0794
Production host: Rhodospirillum rubrum ATCC 11170 (bacteria)
References: UniProt: Q2RW97, nitrogenase
#2: Protein Nitrogenase


Mass: 50856.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Gene: Rru_A0793
Production host: Rhodospirillum rubrum ATCC 11170 (bacteria)
References: UniProt: Q2RW98, nitrogenase
#3: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of marDK heterotetramer under dithionite reduced conditions
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.228 MDa / Experimental value: YES
Source (natural)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria)
Source (recombinant)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria) / Strain: marBHDK deletion strain
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisC4H11NO31
2100 mMsodium chlorideNaCl1
32 mMsodium dithioniteNa2S2O41
SpecimenConc.: 1.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was monodisperse, diluted with buffer from 7.5 mg/mL stock solution.
Specimen supportDetails: 30 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 3.5ul sample was applied to a glow discharged UltrAuFoil grid, blotted for 3 or 4 seconds before plunged in liquid ethane cooled with liquid nitrogen.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Sample was screened using negative staining and Cryo-EM on a screening microscope for sample readiness assessment before automated high-throughput and high-resolution data collection on ...Details: Sample was screened using negative staining and Cryo-EM on a screening microscope for sample readiness assessment before automated high-throughput and high-resolution data collection on Titan Krios. Multiple batches of Cryo-EM specimen were prepared in order to deal with the orientation preference. The calibrated minimum/maximum defocus were the calculated minimum and maximum of images that with contaminants or broken ice.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 109454 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 214 nm / Calibrated defocus max: 3010 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 79.8 K / Temperature (min): 79.8 K
Image recordingAverage exposure time: 2.26 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4840
Details: Data was collected on a ThermoScientific Titan Krios G3i Cryo-TEM operated at 300kV and at a nominal 105,000 magnification using ThermoScientific EPU program with the defocus range of -1.0 ...Details: Data was collected on a ThermoScientific Titan Krios G3i Cryo-TEM operated at 300kV and at a nominal 105,000 magnification using ThermoScientific EPU program with the defocus range of -1.0 to -2.0 um . Image stack files were filtered with a BioQuantum energy filter at 15eV slit width and acquired with a Gatan K3 Direct Electron Detector and (Gatan, Pleasanton, CA, USA) in COunted Super-Resolution mode resulting pixel size 0.4125 angstrom. Total electron dose was 50 electrons. And each stack file consists of 40 frames.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Chromatic aberration corrector: N/A. / Energyfilter slit width: 15 eV / Spherical aberration corrector: N/A.
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.2.1particle selection
2EPU2.12image acquisitionEPU was used for semi automated data collection.
4cryoSPARC4.2.1CTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10ISOLDEmodel refinement
13cryoSPARC4.2.1classification
14cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6195342
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149015 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT)
Details: Final step was actually Non-uniform Refinement of two classes of an Ab Initio reconstruction.
Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: AlphaFold multimer / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.35 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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