8OFO

Structure of Enterococcus faecium CdaA

PDB DOI: https://doi.org/10.2210/pdb8OFO/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus faecium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-16 Released: 2023-06-21
Deposition Author(s): Garbers, T.B., Neumann, P., Ficner, R.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.274
R-Value Work: 0.205

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of Enterococcus faecium CdaA

Garbers, T.B., Neumann, P., Ficner, R.

To be published.

Macromolecule Content

Total Structure Weight: 33.24 kDa
Atom Count: 2,296
Modelled Residue Count: 297
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diadenylate cyclase	A [auth AAA], B [auth BBB]	151	Enterococcus faecium	Mutation(s): 0 Gene Names: dacA
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4G Query on P4G Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA]	C [auth AAA]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.274
R-Value Work: 0.205
Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.16	α = 90
b = 99.16	β = 90
c = 112.18	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-21

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SPP1879

Revision History (Full details and data files)

Version 1.0: 2023-06-21
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.