8S45

CdaA-E05 complex

PDB DOI: https://doi.org/10.2210/pdb8S45/pdb

Classification: PROTEIN BINDING
Organism(s): Listeria monocytogenes
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2024-02-21 Released: 2024-06-19
Deposition Author(s): Neumann, P., Ficner, R.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.236
R-Value Work: 0.196
R-Value Observed: 0.198

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

CdaA-E05 complex

Neumann, P., Ficner, R.

To be published.

Macromolecule Content

Total Structure Weight: 38.99 kDa
Atom Count: 2,604
Modelled Residue Count: 310
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diadenylate cyclase	A, B	178	Listeria monocytogenes	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8Y5E4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G3Y (Subject of Investigation/LOI) Query on G3Y Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	(1~{R},2~{S},3~{S},4~{R},5~{S})-2-azanyl-4-phenylsulfanyl-6,8-dioxabicyclo[3.2.1]octan-3-ol C₁₂ H₁₅ N O₃ S OFCUYBHPAYPQJR-MJDLHHQISA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.236
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.75	α = 90
b = 64.71	β = 90
c = 129.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SPP1879
German Research Foundation (DFG)	Germany	INST186/1117
German Research Foundation (DFG)	Germany	SFB860

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release

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 R01GM157729.