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- PDB-7dfx: Structure and function of Diadenylate cyclase DacM in Mycoplasma ... -

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Basic information

Entry
Database: PDB / ID: 7dfx
TitleStructure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae
ComponentsDAC domain-containing protein
KeywordsIMMUNE SYSTEM / second messenger / c-di-AMP / diadenylate cyclase / Mycoplasma ovipneumoniae
Function / homology
Function and homology information


diadenylate cyclase activity / adenylate cyclase activity / ATP binding / membrane
Similarity search - Function
: / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile.
Similarity search - Domain/homology
MALONIC ACID / DAC domain-containing protein
Similarity search - Component
Biological speciesMycoplasma ovipneumoniae 14811 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.996 Å
AuthorsFan, S. / Li, M.
CitationJournal: To Be Published
Title: Structure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae
Authors: Li, M. / Fan, S.
History
DepositionNov 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DAC domain-containing protein
B: DAC domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5357
Polymers39,0142
Non-polymers5205
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-38 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.075, 192.075, 192.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-432-

HOH

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Components

#1: Protein DAC domain-containing protein / Diadenylate cyclase DacM


Mass: 19507.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma ovipneumoniae 14811 (bacteria)
Gene: MOVI_0530 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: A0A014M399
#2: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 7.54 Å3/Da / Density % sol: 83.69 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 1 M sodium malonate pH 5.0, 0.1 M citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 23720 / % possible obs: 100 % / Redundancy: 36.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.208 / Net I/σ(I): 23
Reflection shellResolution: 3→50 Å / Rmerge(I) obs: 0.208 / Num. unique obs: 23720 / CC1/2: 0.361

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rv7

4rv7


Resolution: 2.996→32.941 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1919 1240 5.23 %
Rwork0.1691 22480 -
obs0.1703 23720 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.79 Å2 / Biso mean: 54.4221 Å2 / Biso min: 18.84 Å2
Refinement stepCycle: final / Resolution: 2.996→32.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 35 85 2574
Biso mean--67.74 48.96 -
Num. residues----314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9961-3.11590.28211530.2593245799
3.1159-3.25760.25671450.2452453100
3.2576-3.42920.22731630.21592472100
3.4292-3.64380.21551480.18182461100
3.6438-3.92470.19081370.16172494100
3.9247-4.31890.17421080.14732529100
4.3189-4.9420.15311100.12762549100
4.942-6.21960.16981280.16222539100
6.2196-32.940.15761480.1524252698

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