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- PDB-9m4e: Cryo-EM structure of Dp42 depolymerase with C3 symmetry against K... -

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Basic information

Entry
Database: PDB / ID: 9m4e
TitleCryo-EM structure of Dp42 depolymerase with C3 symmetry against KN1 serotype Klebsiella pneumoniae,(Dp42-C3)
ComponentsProbable tail spike protein
KeywordsLYASE / Dp42 / depolymerase / cryo-EM / Klebsiella pneumoniae KN1 / capsule polysaccharide LYASE
Function / homologysymbiont entry into host cell via disruption of host cell glycocalyx / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain / symbiont entry into host cell via disruption of host cell envelope / virus tail / adhesion receptor-mediated virion attachment to host cell / Probable tail spike protein
Function and homology information
Biological speciesKlebsiella phage vB_KpnP_IME321 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsXie, Y. / Huang, T. / Shi, X. / Tao, X. / Ma, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200803 China
CitationJournal: To Be Published
Title: Structures and the mechanism investigation of bacteriophage depolymerases for capsular polysaccharide degradation of Klebsiella pneumoniae KN1 serotype
Authors: Xie, Y.
History
DepositionMar 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable tail spike protein
B: Probable tail spike protein
C: Probable tail spike protein


Theoretical massNumber of molelcules
Total (without water)277,2083
Polymers277,2083
Non-polymers00
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

#1: Protein Probable tail spike protein


Mass: 92402.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage vB_KpnP_IME321 (virus)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A344UC14
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: Dp42 with C3 symmetry (Dp42-C3) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Klebsiella phage vB_KpnP_IME321 (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding 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: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 325681 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00514652
ELECTRON MICROSCOPYf_angle_d0.55319974
ELECTRON MICROSCOPYf_dihedral_angle_d4.762076
ELECTRON MICROSCOPYf_chiral_restr0.0482211
ELECTRON MICROSCOPYf_plane_restr0.0052559

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