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- PDB-7l8n: Diadenylate cyclase with AMP from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 7l8n
TitleDiadenylate cyclase with AMP from Streptococcus mutans
ComponentsDiadenylate cyclase
KeywordsTRANSFERASE / cyclase / ATP / AMP / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


diadenylate cyclase / diadenylate cyclase activity / cAMP biosynthetic process / adenylate cyclase activity / ATP binding / plasma membrane
Similarity search - Function
Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / : / 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
ACETATE ION / ADENOSINE MONOPHOSPHATE / MALONATE ION / Diadenylate cyclase
Similarity search - Component
Biological speciesStreptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsHua, Z. / Hui, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE028329 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE022350 United States
CitationJournal: To Be Published
Title: Diadenylate cyclase with AMP from Streptococcus mutans
Authors: Hua, Z. / Hui, W.
History
DepositionDec 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Diadenylate cyclase
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4558
Polymers32,8172
Non-polymers6386
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.360, 84.590, 100.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-491-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Diadenylate cyclase / DAC / Cyclic-di-AMP synthase / c-di-AMP synthase


Mass: 16408.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria)
Strain: ATCC 700610 / UA159 / Gene: dacA, SMU_1428c / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8DTC4, diadenylate cyclase

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Non-polymers , 5 types, 202 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1M sodium malonate pH 5.0, 0.1M sodium acetate trihydrate pH 4.5, 2% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→100 Å / Num. obs: 24283 / % possible obs: 99.8 % / Redundancy: 13.79 % / Biso Wilson estimate: 26.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.46
Reflection shellResolution: 1.94→1.98 Å / Num. unique obs: 8160 / CC1/2: 0.945

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rv7

4rv7


Resolution: 1.94→38.97 Å / SU ML: 0.1787 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 19.5258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2069 2000 8.39 %
Rwork0.1605 21838 -
obs0.1644 23838 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.88 Å2
Refinement stepCycle: LAST / Resolution: 1.94→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2303 0 40 196 2539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01072382
X-RAY DIFFRACTIONf_angle_d1.06153233
X-RAY DIFFRACTIONf_chiral_restr0.0626383
X-RAY DIFFRACTIONf_plane_restr0.0125413
X-RAY DIFFRACTIONf_dihedral_angle_d8.3899330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.27241360.19911484X-RAY DIFFRACTION93.75
1.99-2.040.221350.17821477X-RAY DIFFRACTION93.61
2.04-2.10.19261400.17121524X-RAY DIFFRACTION95.96
2.1-2.170.24461360.17181488X-RAY DIFFRACTION95.42
2.17-2.250.22341400.15721535X-RAY DIFFRACTION96.99
2.25-2.340.22321410.15491527X-RAY DIFFRACTION97.26
2.34-2.440.19891400.15811529X-RAY DIFFRACTION96.53
2.44-2.570.22841450.16451583X-RAY DIFFRACTION98.97
2.57-2.730.24341440.16041575X-RAY DIFFRACTION99.59
2.73-2.950.22961440.16761581X-RAY DIFFRACTION99.71
2.95-3.240.19721480.17931603X-RAY DIFFRACTION99.83
3.24-3.710.1931470.15511606X-RAY DIFFRACTION99.72
3.71-4.670.17571480.13171625X-RAY DIFFRACTION100
4.67-38.970.20481560.16941701X-RAY DIFFRACTION99.73

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