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- PDB-9k4b: Cryo-EM structure of depolymerase S2-4 from Klebsiella phage K64-1 -

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Basic information

Entry
Database: PDB / ID: 9k4b
TitleCryo-EM structure of depolymerase S2-4 from Klebsiella phage K64-1
ComponentsDepolymerase, capsule K1-specific
KeywordsANTIMICROBIAL PROTEIN / Depolymerase / Degradation of host capsule
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / adhesion receptor-mediated virion attachment to host cell / lyase activity
Similarity search - Function
: / : / K1 capsule-specific polysaccharide lyase, C-terminal domain / K1 capsule-specific polysaccharide lyase, Rider domain / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Depolymerase, capsule K1-specific
Similarity search - Component
Biological speciesKlebsiella phage K64-1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsZhao, R. / Du, T. / Ren, Z. / Gu, J. / Ru, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32072824 China
National Natural Science Foundation of China (NSFC)32222083 China
CitationJournal: Microbiol Res / Year: 2026
Title: Characterization of the phage Phi K64 depolymerase S2-4 and its therapeutic effect against K1 serotype Klebsiella pneumoniae.
Authors: Zhao, R. / Du, T. / Ji, Y. / Ren, Z. / Jiang, S. / Ru, H. / Gu, J.
History
DepositionOct 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 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: Depolymerase, capsule K1-specific
B: Depolymerase, capsule K1-specific
C: Depolymerase, capsule K1-specific


Theoretical massNumber of molelcules
Total (without water)302,9883
Polymers302,9883
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 Depolymerase, capsule K1-specific / Probable tail fiber protein


Mass: 100996.148 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage K64-1 (virus) / Gene: S2-4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A8J8T2
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: Depolymerase S2-4 homotrimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Klebsiella phage K64-1 (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
SpecimenConc.: 1 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: 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: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4015926 / Symmetry type: POINT
RefinementResolution: 2.18→273.92 Å / SU ML: 0.11 / σ(F): 0.07 / Phase error: 45.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.322 1993 0.05 %
Rwork0.3125 --
obs0.3125 4150106 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00815705
ELECTRON MICROSCOPYf_angle_d0.95821333
ELECTRON MICROSCOPYf_dihedral_angle_d8.432169
ELECTRON MICROSCOPYf_chiral_restr0.062481
ELECTRON MICROSCOPYf_plane_restr0.0062748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.230.60631440.6713294557ELECTRON MICROSCOPY99
2.23-2.290.59231440.5509295860ELECTRON MICROSCOPY100
2.29-2.360.51441430.5404297206ELECTRON MICROSCOPY100
2.36-2.440.55681560.5203295371ELECTRON MICROSCOPY100
2.44-2.530.54511320.4959296957ELECTRON MICROSCOPY100
2.53-2.630.48951200.4523296559ELECTRON MICROSCOPY100
2.63-2.750.42151670.4202296748ELECTRON MICROSCOPY100
2.75-2.890.41191440.3791296109ELECTRON MICROSCOPY100
2.89-3.070.38221200.346296587ELECTRON MICROSCOPY100
3.07-3.310.27241680.3113297265ELECTRON MICROSCOPY100
3.31-3.640.30611440.2625296106ELECTRON MICROSCOPY100
3.64-4.170.21631440.2362296546ELECTRON MICROSCOPY100
4.17-5.250.22441200.1975296587ELECTRON MICROSCOPY100
5.26-273.920.21391470.2036295655ELECTRON MICROSCOPY100

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