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- PDB-7dg0: Structure and function of Diadenylate cyclase DacM in Mycoplasma ... -

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Basic information

Entry
Database: PDB / ID: 7dg0
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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DAC domain-containing protein
Similarity search - Component
Biological speciesMycoplasma ovipneumoniae 14811 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.895 Å
AuthorsFan, S.L.
CitationJournal: To Be Published
Title: Structure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae
Authors: Li, M. / Fan, S.L.
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)40,2254
Polymers39,2912
Non-polymers9342
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-13 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.057, 68.683, 113.353
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19645.291 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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 19% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 24587 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Net I/σ(I): 28.1
Reflection shellResolution: 1.89→1.97 Å / Rmerge(I) obs: 0.084 / Num. unique obs: 24587 / CC1/2: 0.995

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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: 1.895→26.196 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 1263 5.14 %
Rwork0.1731 23324 -
obs0.1749 24587 93.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.01 Å2 / Biso mean: 28.7619 Å2 / Biso min: 5.55 Å2
Refinement stepCycle: final / Resolution: 1.895→26.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 58 240 2724
Biso mean--54.96 38.55 -
Num. residues----310
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8952-1.97110.2834980.2281176765
1.9711-2.06080.24111310.2044225883
2.0608-2.16940.22121110.1851264496
2.1694-2.30520.21811690.176266499
2.3052-2.48310.20521260.17592748100
2.4831-2.73270.21411530.17352759100
2.7327-3.12760.22091590.17762758100
3.1276-3.93830.18111570.15682781100
3.9383-26.190.19981590.16332945100
Refinement TLS params.Method: refined / Origin x: -16.0478 Å / Origin y: -1.597 Å / Origin z: 17.8892 Å
111213212223313233
T0.0439 Å20.022 Å2-0.0556 Å2-0.0384 Å2-0.0429 Å2--0.1028 Å2
L2.0503 °20.0829 °2-0.7561 °2-1.4376 °20.1413 °2--3.0846 °2
S0.0365 Å °0.0755 Å °-0.1107 Å °-0.0379 Å °-0.006 Å °-0.0476 Å °-0.1112 Å °-0.1487 Å °-0.0246 Å °
Refinement TLS groupSelection details: all

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