6K6T | pdb_00006k6t

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form

• PDB DOI: https://doi.org/10.2210/pdb6K6T/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae O395
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-06-04 Released: 2020-06-17 
• Deposition Author(s): Yadav, M., Pal, K., Sen, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form

Yadav, M., Pal, K., Sen, U.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 119.06 kDa 
• Atom Count: 8,196 
• Modeled Residue Count: 948 
• Deposited Residue Count: 1,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EAL domain protein	A, B, C, D	257	Vibrio cholerae O395	Mutation(s): 1  Gene Names: VC0395_A1247 EC: 3.1.4.1
UniProt
Find proteins for A0A0H3AJ04 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AJ04  Go to UniProtKB:  A0A0H3AJ04

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2I (Subject of Investigation/LOI)	E [auth A], H [auth B], K [auth C], N [auth D]	9-[(1R,6R,8R,9S,10R,15S,17R,18S)-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-17-(6-oxidanylidene-3H-purin-9-yl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-3H-purin-6-one C20 H22 N8 O14 P2 VFTRASQVWRBMKD-PHSICLOESA-N
CA (Subject of Investigation/LOI)	F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.45	α = 90
b = 42.54	β = 94.65
c = 155.04	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Yadav, M., Pal, K., Sen, U.

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description