7TWE

Crystal Structure of the Putative Oxidoreductase of DUF1479-containing Protein Family YPO2976 from Yersinia pestis Bound to 2-oxo-glutaric acid

• PDB DOI: https://doi.org/10.2210/pdb7TWE/pdb

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


• Deposited: 2022-02-07 Released: 2022-02-16 
• 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: 2.41 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Crystal Structure of the Putative Oxidoreductase of DUF1479-containing Protein Family YPO2976 from Yersinia pestis Bound to 2-oxo-glutaric acid

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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 95.5 kDa 
• Atom Count: 6,557 
• Modelled Residue Count: 804 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF1479 domain-containing protein	A, B	418	Yersinia pestis CO92	Mutation(s): 0  Gene Names: YPO2976
UniProt
Find proteins for A0A2U2H2N4 (Yersinia pestis) Explore A0A2U2H2N4  Go to UniProtKB:  A0A2U2H2N4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG (Subject of Investigation/LOI)	D [auth A], F [auth B]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
EDO	G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.236 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.426	α = 90
b = 54.054	β = 92.971
c = 148.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-16 
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: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection