6HVN

CdaA-APO Y187A Mutant

• PDB DOI: https://doi.org/10.2210/pdb6HVN/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-10-11 Released: 2019-06-05 
• Deposition Author(s): Heidemann, J.L., Neumann, P., Ficner, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

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)

Macromolecule Content

• Total Structure Weight: 39.18 kDa 
• Atom Count: 2,725 
• Modelled Residue Count: 334 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diadenylate cyclase	A, B	178	Listeria monocytogenes EGD-e	Mutation(s): 1  Gene Names: dacA, cdaA, lmo2120 EC: 2.7.7.85
UniProt
Find proteins for Q8Y5E4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y5E4  Go to UniProtKB:  Q8Y5E4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.49	α = 90
b = 65.13	β = 90
c = 131.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-05 
Deposition Author(s): Heidemann, J.L., Neumann, P., Ficner, R.

---

Funding Organization	Location	Grant Number
	Germany	--

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary