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- PDB-23py: N-His tagged YghJ protein substrate-accessible state -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 23py
TitleN-His tagged YghJ protein substrate-accessible state
ComponentsPutative lipoprotein AcfD homolog
KeywordsHYDROLASE / active enzyme / mucinase / O-glycoprotease
Function / homology
Function and homology information


transmembrane transporter binding / plasma membrane
Similarity search - Function
Domain of unknown function DUF4092 / Domain of unknown function (DUF4092) / AcfD helical domain / M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / : / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. ...Domain of unknown function DUF4092 / Domain of unknown function (DUF4092) / AcfD helical domain / M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / : / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Putative lipoprotein AcfD homolog
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsGu, J.K. / Zhang, M.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270832 China
CitationJournal: Protein Cell / Year: 2026
Title: Molecular basis for zymogen-like autoinhibition of the M60-like metallopeptidase YghJ.
Authors: Minghui Zhang / Bowen Wu / Zhouzhu Liang / Yintao Su / Huacai Peng / Jinke Gu /
History
DepositionFeb 12, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 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: Putative lipoprotein AcfD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,4702
Polymers167,4051
Non-polymers651
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 Putative lipoprotein AcfD homolog


Mass: 167405.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: yghJ, b4466, JW5925, ECK2968 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CK95
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: N-His tagged YghJ substrate-accessible state / Type: CELL / Entity ID: #1 / Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280499 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038687
ELECTRON MICROSCOPYf_angle_d0.5811797
ELECTRON MICROSCOPYf_dihedral_angle_d4.8061168
ELECTRON MICROSCOPYf_chiral_restr0.0431246
ELECTRON MICROSCOPYf_plane_restr0.0051555

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