7THW

Crystal Structure of the Soluble Domain of the Putative OmpA -Family Membrane Protein YPO0514 from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb7THW/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-12 Released: 2022-01-26 
• Deposition Author(s): Kim, Y., Tesar, C., Chhor, G., Clancy, S., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.269 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

Crystal Structure of the Soluble Domain of the Putative OmpA -Family Membrane Protein YPO0514 from Yersinia pestis

Kim, Y., Tesar, C., Chhor, G., Clancy, S., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 89.61 kDa 
• Atom Count: 5,021 
• Modelled Residue Count: 603 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative OmpA-family membrane protein	A, B, C, D	190	Yersinia pestis CO92	Mutation(s): 0  Gene Names: YPO0514
UniProt
Find proteins for A0A454Y5W9 (Yersinia pestis) Explore A0A454Y5W9  Go to UniProtKB:  A0A454Y5W9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	I [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.269 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.861	α = 90
b = 123.099	β = 89.965
c = 54.183	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Kim, Y., Tesar, C., Chhor, G., Clancy, S., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release