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- PDB-8kic: Bacterial serine protease -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8kic
TitleBacterial serine protease
Components
  • (Lysozyme fragment (unknown sequence)) x 3
  • peptidase Do
KeywordsHYDROLASE / Seine protease
Function / homology
Function and homology information


peptidase Do / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsLee, I.-G. / Jeon, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other privateLF-RSP2022-02 Korea, Republic Of
CitationJournal: To Be Published
Title: Structure of bacterial serine protease
Authors: Lee, I.-G. / Jeon, H.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 4, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: peptidase Do
E: peptidase Do
F: peptidase Do
C: peptidase Do
A: peptidase Do
B: peptidase Do
G: Lysozyme fragment (unknown sequence)
H: Lysozyme fragment (unknown sequence)
I: Lysozyme fragment (unknown sequence)


Theoretical massNumber of molelcules
Total (without water)291,9229
Polymers291,9229
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
peptidase Do


Mass: 48361.047 Da / Num. of mol.: 6 / Mutation: S214A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: degQ / Production host: Escherichia coli (E. coli) / References: UniProt: C3SRW2
#2: Protein/peptide Lysozyme fragment (unknown sequence)


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: egg white / Plasmid details: purified from chicken egg white
#3: Protein/peptide Lysozyme fragment (unknown sequence)


Mass: 443.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: egg white
#4: Protein/peptide Lysozyme fragment (unknown sequence)


Mass: 613.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: Chichken egg white
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: Bacterial serine protease-lysozyme complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 67.7 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 382427 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048619
ELECTRON MICROSCOPYf_angle_d0.65711637
ELECTRON MICROSCOPYf_dihedral_angle_d4.541221
ELECTRON MICROSCOPYf_chiral_restr0.0471401
ELECTRON MICROSCOPYf_plane_restr0.0051533

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