7D62 | pdb_00007d62

pGpG-specific phosphodiesterase - PggH from Vibrio cholrae

• PDB DOI: https://doi.org/10.2210/pdb7D62/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-28 Released: 2020-10-28 
• Deposition Author(s): Ha, N.-C., Jang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

A pGpG-specific phosphodiesterase

Lee, J.-W., Heo, K., Jang, Y., Ha, N.-C., Seok, Y.-J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 74.32 kDa 
• Atom Count: 4,796 
• Modeled Residue Count: 587 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PggH	A, B	324	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_A0593
UniProt
Find proteins for Q9KLZ6 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KLZ6  Go to UniProtKB:  Q9KLZ6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN (Subject of Investigation/LOI)	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.367	α = 90
b = 148.83	β = 90
c = 58.845	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): Ha, N.-C., Jang, Y.

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references