4RDB

Crystal structure of an immunoreactive 32 kDa antigen PG49 (PG_0181) from Porphyromonas gingivalis W83 at 1.45 A resolution (PSI Community Target, Nakayama)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.119 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Distinct Type of Pilus from the Human Microbiome.

Xu, Q.Shoji, M.Shibata, S.Naito, M.Sato, K.Elsliger, M.A.Grant, J.C.Axelrod, H.L.Chiu, H.J.Farr, C.L.Jaroszewski, L.Knuth, M.W.Deacon, A.M.Godzik, A.Lesley, S.A.Curtis, M.A.Nakayama, K.Wilson, I.A.

(2016) Cell 165: 690-703

  • DOI: 10.1016/j.cell.2016.03.016
  • Primary Citation of Related Structures:  
    3T2L, 3SY6, 3UFI, 3UP6, 4H40, 4GPV, 4Q98, 4QB7, 4QDG, 4JG5

  • PubMed Abstract: 
  • Pili are proteinaceous polymers of linked pilins that protrude from the cell surface of many bacteria and often mediate adherence and virulence. We investigated a set of 20 Bacteroidia pilins from the human microbiome whose structures and mechanism o ...

    Pili are proteinaceous polymers of linked pilins that protrude from the cell surface of many bacteria and often mediate adherence and virulence. We investigated a set of 20 Bacteroidia pilins from the human microbiome whose structures and mechanism of assembly were unknown. Crystal structures and biochemical data revealed a diverse protein superfamily with a common Greek-key β sandwich fold with two transthyretin-like repeats that polymerize into a pilus through a strand-exchange mechanism. The assembly mechanism of the central, structural pilins involves proteinase-assisted removal of their N-terminal β strand, creating an extended hydrophobic groove that binds the C-terminal donor strands of the incoming pilin. Accessory pilins at the tip and base have unique structural features specific to their location, allowing initiation or termination of the assembly. The Bacteroidia pilus, therefore, has a biogenesis mechanism that is distinct from other known pili and likely represents a different type of bacterial pilus.


    Organizational Affiliation

    Joint Center for Structural Genomics, http://www.jcsg.org; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Immunoreactive 32 kDa antigen PG49A305Porphyromonas gingivalis W83Mutation(s): 0 
Gene Names: PG_0181mfA4
Find proteins for Q7MXK0 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MXK0 
Go to UniProtKB:  Q7MXK0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACN
Query on ACN

Download CCD File 
A
ACETONE
C3 H6 O
CSCPPACGZOOCGX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.117 
  • R-Value Observed: 0.119 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.636α = 90
b = 86.821β = 90
c = 90.645γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2018-01-24
    Changes: Database references
  • Version 1.3: 2020-04-22
    Changes: Database references, Derived calculations