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- PDB-8w69: DegQ-b-casein complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8w69
TitleDegQ-b-casein complex
Components
  • (Casein fragment) x 2
  • peptidase Do
KeywordsHYDROLASE / Complex
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)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLee, I.-G. / Jeon, H.
Funding support1items
OrganizationGrant numberCountry
Other privateLF-RSP2022-02
CitationJournal: To Be Published
Title: Structure of E. coli Deg-b-casein complex
Authors: Lee, I.-G. / Jeon, H.
History
DepositionAug 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 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
A: peptidase Do
C: peptidase Do
B: peptidase Do
D: peptidase Do
F: peptidase Do
E: peptidase Do
G: Casein fragment
H: Casein fragment
I: Casein fragment


Theoretical massNumber of molelcules
Total (without water)292,1789
Polymers292,1789
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
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C3SRW2
#2: Protein/peptide Casein fragment


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We would like to assign these residues as unknown (UNK).
Source: (natural) Bos taurus (domestic cattle) / Plasmid details: Purified from bovine milk
#3: Protein/peptide Casein fragment


Mass: 613.749 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: We would like to assign these residues as unknown (UNK)
Source: (natural) Bos taurus (domestic cattle) / Plasmid details: Purified from bovine milk
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DegQ-beta casein complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048619
ELECTRON MICROSCOPYf_angle_d0.67711637
ELECTRON MICROSCOPYf_dihedral_angle_d4.071221
ELECTRON MICROSCOPYf_chiral_restr0.0461401
ELECTRON MICROSCOPYf_plane_restr0.0071533

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