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- PDB-9l2i: Cryo-EM structure of soluble methane monooxygenase hydroxylase fr... -

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Basic information

Entry
Database: PDB / ID: 9l2i
TitleCryo-EM structure of soluble methane monooxygenase hydroxylase from Methylosinus sporium 5
Components(Methane monooxygenase) x 3
KeywordsOXIDOREDUCTASE / soluble methane monoxoygenase / hydroxylase / homodimer
Function / homology
Function and homology information


methane metabolic process / methane monooxygenase [NAD(P)H] activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / monooxygenase activity / metal ion binding
Similarity search - Function
Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase ...Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Methane monooxygenase / Methane monooxygenase / Methane monooxygenase
Similarity search - Component
Biological speciesMethylosinus sporium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsHwang, Y. / Pozharski, E. / Lee, S.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2023RIS-008 Korea, Republic Of
Ministry of Education (MoE, Korea)2017R1A6A1A03015876 Korea, Republic Of
CitationJournal: To be published
Title: Complex formation via regulatory component of MMOH from Methylosinus sporium 5
Authors: Hwang, Y. / Pozharski, E. / Lee, S.J.
History
DepositionDec 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methane monooxygenase
B: Methane monooxygenase
C: Methane monooxygenase
D: Methane monooxygenase
E: Methane monooxygenase
F: Methane monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,41910
Polymers249,1956
Non-polymers2234
Water1086
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 Methane monooxygenase / MmoX1 / Alpha-subunit


Mass: 59979.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylosinus sporium (bacteria) / References: UniProt: Q27RN7
#2: Protein Methane monooxygenase / MmoY / Beta-subunit


Mass: 45239.246 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylosinus sporium (bacteria) / References: UniProt: Q27RN6
#3: Protein Methane monooxygenase / MmoZ / Gamma-subunit


Mass: 19379.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylosinus sporium (bacteria) / References: UniProt: Q27RN4
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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 MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of soluble methane monooxygenase hydroxylase
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Methylosinus sporium (bacteria)
Buffer solutionpH: 6.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 250 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 36.6 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.2particle selection
4cryoSPARC3.3.2CTF correction
7PHENIX1.19.2-4158model fitting
9PHENIX1.19.2-4158model refinement
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
12cryoSPARC3.3.2classification
13cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 374590
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60960 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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