4JRF | pdb_00004jrf

Crystal structure of a putative cell adhesion protein (BACOVA_01548) from Bacteroides ovatus ATCC 8483 at 1.98 A resolution (PSI Community Target, Nakayama)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.178 (Depositor), 0.158 (DCC) 
  • R-Value Work: 
    0.155 (Depositor) 
  • R-Value Observed: 
    0.157 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4JRF

This is version 1.5 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: https://doi.org/10.1016/j.cell.2016.03.016
  • Primary Citation Related Structures: 
    3LIU, 3PAY, 3R4R, 3SY6, 3T2L, 3UFI, 3UP6, 4DGU, 4EPS, 4GPV, 4H40, 4JG5, 4JRF, 4K4K, 4Q98, 4QB7, 4QDG, 4RDB, 5CAG

  • 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 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; SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA.

Macromolecule Content 

  • Total Structure Weight: 55.95 kDa 
  • Atom Count: 4,036 
  • Modeled Residue Count: 479 
  • Deposited Residue Count: 508 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
putative cell adhesion protein508Bacteroides ovatus ATCC 8483Mutation(s): 0 
Gene Names: ZP_02064579.1

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.178 (Depositor), 0.158 (DCC) 
  • R-Value Work:  0.155 (Depositor) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.022α = 90
b = 134.022β = 90
c = 57.73γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNTrefinement
XDSdata reduction
SHELXDphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2018-01-24
    Changes: Database references
  • Version 1.3: 2020-04-22
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-11-06
    Changes: Data collection, Structure summary