5LDY | pdb_00005ldy

Structure of Yersinia pseudotuberculosis InvD

• PDB DOI: https://doi.org/10.2210/pdb5LDY/pdb

• Classification: CELL ADHESION
• Organism(s): Yersinia pseudotuberculosis YPIII
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-28 Released: 2017-06-14 
• Deposition Author(s): Sadana, P., Scrima, A.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.253 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

The invasin D protein from Yersinia pseudotuberculosis selectively binds the Fab region of host antibodies and affects colonization of the intestine

Sadana, P., Geyer, R., Pezoldt, J., Helmsing, S., Huehn, J., Hust, M., Dersch, P., Scrima, A.

(2018) J Biol Chem 

• DOI: https://doi.org/10.1074/jbc.RA117.001068

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 74.02 kDa 
• Atom Count: 4,943 
• Modeled Residue Count: 674 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig domain protein group 1 domain protein	A, B	357	Yersinia pseudotuberculosis YPIII	Mutation(s): 0  Gene Names: YPK_1315
UniProt
Find proteins for A0A0H3B1G5 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII)) Explore A0A0H3B1G5  Go to UniProtKB:  A0A0H3B1G5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.253 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.9	α = 90
b = 58.9	β = 90
c = 274.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Sadana, P., Scrima, A.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	VH-NG-727
Helmholtz Association	Germany	VH-GS-202

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2020-06-17
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Structure summary