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- PDB-44fh: Hexadecameric complex of serine proteinase(SDH) -

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Basic information

Entry
Database: PDB / ID: 44fh
TitleHexadecameric complex of serine proteinase(SDH)
Componentsserine proteinase(SDH)
KeywordsIMMUNE SYSTEM / hexadecamer
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsYu, Y. / Chen, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Passive abortive infection mechanisms targeting phage long tail fiber proteins
Authors: Yu, Y. / Chen, J.
History
DepositionJul 27, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 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

Downloads & links

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Assembly

Deposited unit
M: serine proteinase(SDH)
N: serine proteinase(SDH)
O: serine proteinase(SDH)
P: serine proteinase(SDH)
A: serine proteinase(SDH)
B: serine proteinase(SDH)
C: serine proteinase(SDH)
D: serine proteinase(SDH)
E: serine proteinase(SDH)
F: serine proteinase(SDH)
G: serine proteinase(SDH)
H: serine proteinase(SDH)
I: serine proteinase(SDH)
J: serine proteinase(SDH)
K: serine proteinase(SDH)
L: serine proteinase(SDH)


Theoretical massNumber of molelcules
Total (without water)541,83016
Polymers541,83016
Non-polymers00
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
serine proteinase(SDH)


Mass: 33864.375 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
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: Hexadecameric complex of serine proteinase(SDH) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
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: 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: 8293 nm / Nominal defocus min: 2945 nm
Image recordingElectron dose: 62.48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIX1.15.2_3472model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 837848 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00973982
ELECTRON MICROSCOPYf_angle_d0.773133777
ELECTRON MICROSCOPYf_dihedral_angle_d11.45929731
ELECTRON MICROSCOPYf_chiral_restr0.0565822
ELECTRON MICROSCOPYf_plane_restr0.00511067

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