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- PDB-9dxf: attLmm bound serine integrase and RDF complex in the post-rotatio... -

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Basic information

Entry
Database: PDB / ID: 9dxf
TitleattLmm bound serine integrase and RDF complex in the post-rotation state
Components
  • DNA (24-MER)
  • DNA (25-MER)
  • DNA (33-MER)
  • DNA (34-MER)
  • Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
KeywordsDNA BINDING PROTEIN / Viral protein / Integrase / Recombinase / Complex / Recombination Directionality Factor / Integration / Excision
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA recombination / DNA binding
Similarity search - Function
Recombinase / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain
Similarity search - Domain/homology
DNA / DNA (> 10) / Resolvase homolog YokA / SPbeta prophage-derived uncharacterized protein YotN
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsShin, H. / Rice, P.A. / Olorunniji, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Structural Basis of Directionality Control in Large Serine Integrases
Authors: Shin, H.S. / Rice, P.A.
History
DepositionOct 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data 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: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
B: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
C: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
D: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
E: DNA (34-MER)
F: DNA (33-MER)
G: DNA (25-MER)
H: DNA (24-MER)
I: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
J: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
K: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
L: Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN
M: DNA (34-MER)
N: DNA (33-MER)
O: DNA (25-MER)
P: DNA (24-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)644,01120
Polymers643,75016
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA chain , 4 types, 8 molecules EMFNGOHP

#2: DNA chain DNA (34-MER)


Mass: 10433.742 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#3: DNA chain DNA (33-MER)


Mass: 10161.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#4: DNA chain DNA (25-MER)


Mass: 7655.984 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#5: DNA chain DNA (24-MER)


Mass: 7382.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)

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Protein / Non-polymers , 2 types, 12 molecules ABCDIJKL

#1: Protein
Resolvase homolog YokA,SPbeta prophage-derived uncharacterized protein YotN


Mass: 71560.180 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yokA, BSU21660, yotN, yokJ, BSU19820
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O32006, UniProt: O34850
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

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: attLmm bound serine integrase and RDF complex in the pre-rotation state
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: vitreous ice
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210561 / Symmetry type: POINT

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