7DFX | pdb_00007dfx

Structure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae

• PDB DOI: https://doi.org/10.2210/pdb7DFX/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mesomycoplasma ovipneumoniae 14811
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): No 


• Deposited: 2020-11-10 Released: 2021-11-17 
• Deposition Author(s): Fan, S., Li, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.192 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae

Li, M., Fan, S.

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

Macromolecule Content 

• Total Structure Weight: 39.53 kDa 
• Atom Count: 2,590 
• Modeled Residue Count: 314 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DAC domain-containing protein	A, B	174	Mesomycoplasma ovipneumoniae 14811	Mutation(s): 0  Gene Names: MOVI_0530
UniProt
Find proteins for A0A014M399 (Mesomycoplasma ovipneumoniae 14811) Explore A0A014M399  Go to UniProtKB:  A0A014M399

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.192 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.075	α = 90
b = 192.075	β = 90
c = 192.075	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Fan, S., Li, M.

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary