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

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)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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 Biological Chem

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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3B1G5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-06-14

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.