7DG0 | pdb_00007dg0

Structure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae

• PDB DOI: https://doi.org/10.2210/pdb7DG0/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.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae

Li, M., Fan, S.L.

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: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 40.22 kDa 
• Atom Count: 2,767 
• Modeled Residue Count: 310 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DAC domain-containing protein	A, B	175	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)	D [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.057	α = 90
b = 68.683	β = 90
c = 113.353	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.L.

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description