7TFQ

Crystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK Bound to Copper Ion from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb7TFQ/pdb

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


• Deposited: 2022-01-07 Released: 2022-01-19 
• Deposition Author(s): Kim, Y., Chhor, G., Endres, M., 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.196 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

Literature

Crystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK Bound to Copper Ion from Yersinia pestis

Kim, Y., Chhor, G., Endres, M., 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.

Macromolecule Content

• Total Structure Weight: 32.54 kDa 
• Atom Count: 2,460 
• Modelled Residue Count: 284 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pirin family protein Yhak	A	292	Yersinia pestis CO92	Mutation(s): 0  Gene Names: YP_1950, EGX46_10965
UniProt
Find proteins for A0A2U2H063 (Yersinia pestis) Explore A0A2U2H063  Go to UniProtKB:  A0A2U2H063

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN	E [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	F [auth A], G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.196 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.133	α = 90
b = 100.737	β = 90
c = 45.498	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-19 
Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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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: 2022-01-19
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Structure summary