8S49 | pdb_00008s49

CdaA-B06 complex

PDB DOI: https://doi.org/10.2210/pdb8S49/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: 1.70 Å
R-Value Free:
0.221 (Depositor), 0.230 (DCC)
R-Value Work:
0.197 (Depositor), 0.202 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

CdaA-B06 complex

Neumann, P., Ficner, R.

To be published.

Macromolecule Content

Total Structure Weight: 38.95 kDa
Atom Count: 2,532
Modeled Residue Count: 308
Deposited Residue Count: 356
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y5E4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
45Y (Subject of Investigation/LOI) Query on 45Y Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	2-(4-fluorophenyl)acetohydrazide C₈ H₉ F N₂ O PFBNINAURUGQRR-UHFFFAOYSA-N		Interactions Focus chain E [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.221 (Depositor), 0.230 (DCC)
R-Value Work: 0.197 (Depositor), 0.202 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.66	α = 90
b = 64.75	β = 90
c = 129.06	γ = 90

Software Package:

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

Structure Validation

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.