5EQV | pdb_00005eqv

1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site

• PDB DOI: https://doi.org/10.2210/pdb5EQV/pdb

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


• Deposited: 2015-11-13 Released: 2015-11-25 
• Deposition Author(s): Minasov, G., Shuvalova, L., Brunzelle, J.S., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.153 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

1.45 Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site.

Minasov, G., Shuvalova, L., Brunzelle, J.S., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.8 kDa 
• Atom Count: 3,487 
• Modeled Residue Count: 336 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein	A	340	Yersinia pestis CO92	Mutation(s): 0  Gene Names: cpdB, AK38_3205 EC: 3.1.4.16 (PDB Primary Data), 3.1.3.6 (UniProt)
UniProt
Find proteins for A0A5P8YBY3 (Yersinia pestis) Explore A0A5P8YBY3  Go to UniProtKB:  A0A5P8YBY3

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	H [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MLT	G [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
TRS	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
FE	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA	D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.153 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35eqv

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.282	α = 90
b = 107.282	β = 90
c = 63.357	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
BLU-MAX	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Minasov, G., Shuvalova, L., Brunzelle, J.S., Kiryukhina, O., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary