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- PDB-9mzu: Structure of PorKN from Porphyromonas gingivalis -

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Basic information

Entry
Database: PDB / ID: 9mzu
TitleStructure of PorKN from Porphyromonas gingivalis
Components
  • Gliding motility protein GldN
  • PorK
KeywordsPROTEIN TRANSPORT / T9SS Type 9 Secretion System C33 assembly periplasmic assembly membrane protein
Function / homology
Function and homology information


formylglycine-generating oxidase activity
Similarity search - Function
Gliding motility associated protein GldN / Gliding motility associated protein GldN / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
alpha-D-mannopyranose / Gliding motility protein GldN / Lipoprotein, putative
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsLea, S.M. / Deme, J.C. / Berks, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: A central role for disulfide bonds in Bacteroidota protein transportation and gliding motility
Authors: Liu, X. / Avaramova, M. / Deme, J.C. / Lundgren, C. / Jones, R.M. / Lea, S.M. / Berks, B.C.
History
DepositionJan 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Mask / Part number: 2 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data 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: PorK
B: Gliding motility protein GldN
C: PorK
D: Gliding motility protein GldN
E: PorK
F: Gliding motility protein GldN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,15621
Polymers293,0906
Non-polymers6,06515
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein PorK


Mass: 55967.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / Strain: (strain ATCC BAA-308 / W83) / References: UniProt: Q7MXB7
#2: Protein Gliding motility protein GldN


Mass: 41729.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / Strain: (strain ATCC BAA-308 / W83) / References: UniProt: Q7MXB4

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Sugars , 2 types, 12 molecules

#3: Polysaccharide
alpha-L-fucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L- ...alpha-L-fucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 810.702 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-4DGlcpa1-4DGlcpAa1-2[LRhapa1-4]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,5,4/[a1122h-1a_1-5][a2122A-1a_1-5][a2122h-1a_1-5][a1221m-1a_1-5][a2211m-1a_1-5]/1-2-3-4-5/a2-b1_a4-e1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-GlcpA]{[(4+1)][a-D-Glcp]{[(4+1)][a-L-Fucp]{}}}[(4+1)][a-L-Rhap]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 6 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: PorKN / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
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: 2000 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: dev_5430 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 676608 / Symmetry type: POINT
RefinementHighest resolution: 2.4 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317988
ELECTRON MICROSCOPYf_angle_d0.48124429
ELECTRON MICROSCOPYf_dihedral_angle_d8.3463117
ELECTRON MICROSCOPYf_chiral_restr0.0412649
ELECTRON MICROSCOPYf_plane_restr0.0033147

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