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- PDB-8ofg: Streptococcus pneumoniae CdaA in complex with c-di-amp -

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Basic information

Entry
Database: PDB / ID: 8ofg
TitleStreptococcus pneumoniae CdaA in complex with c-di-amp
Components
  • Diadenylate cyclase
  • GLU-ARG-LEU-LEU-GLY-GLY-TRP-LYS
KeywordsTRANSFERASE / diadenylate cyclase
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
ADENOSINE MONOPHOSPHATE / Diadenylate cyclase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGarbers, T.B. / Neumann, P. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP 1879 Germany
CitationJournal: To Be Published
Title: Streptococcus pneumoniae CdaA in complex with c-di-amp
Authors: Garbers, T.B. / Neumann, P. / Ficner, R.
History
DepositionMar 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diadenylate cyclase
B: Diadenylate cyclase
C: GLU-ARG-LEU-LEU-GLY-GLY-TRP-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5745
Polymers41,2023
Non-polymers3722
Water50428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-15 kcal/mol
Surface area14620 Å2
Unit cell
Length a, b, c (Å)86.570, 86.570, 110.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Diadenylate cyclase


Mass: 20121.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: dacA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DP14
#2: Protein/peptide GLU-ARG-LEU-LEU-GLY-GLY-TRP-LYS


Mass: 960.132 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris/HCl pH 8.5 4.5 M NaCl / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 17076 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 57.32 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.264 / Rrim(I) all: 0.271 / Net I/σ(I): 8.07
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.4-2.461.59612190.6981.6341
2.46-2.531.23812020.831.2681
2.53-2.61.06111700.8111.0871
2.6-2.680.81711330.8670.8371
2.68-2.770.62211140.930.6371
2.77-2.870.55410680.9450.5681
2.87-2.980.44710500.9680.4591
2.98-3.10.3719880.9710.3811
3.1-3.240.3219620.9790.3291
3.24-3.390.2879130.9680.2951
3.39-3.580.2598870.9780.2681
3.58-3.790.2538370.9820.261
3.79-4.060.2437800.9870.2481
4.06-4.380.237550.9860.2361
4.38-4.80.2246850.9890.231
4.8-5.370.2276290.9860.2331
5.37-6.20.2295610.980.2351
6.2-7.590.2224820.9860.2281
7.59-10.730.2153980.990.2211

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.28 Å / SU ML: 0.334 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.1861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2521 861 5.06 %
Rwork0.2237 16164 -
obs0.2254 17025 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.79 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 23 28 2462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882471
X-RAY DIFFRACTIONf_angle_d1.06473342
X-RAY DIFFRACTIONf_chiral_restr0.0605401
X-RAY DIFFRACTIONf_plane_restr0.0091418
X-RAY DIFFRACTIONf_dihedral_angle_d8.979343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.34391460.30632630X-RAY DIFFRACTION100
2.55-2.750.36871160.29992645X-RAY DIFFRACTION99.89
2.75-3.020.33881540.27782640X-RAY DIFFRACTION100
3.02-3.460.30011330.26582692X-RAY DIFFRACTION99.89
3.46-4.360.23111430.19352710X-RAY DIFFRACTION99.93
4.36-43.280.20481690.19232847X-RAY DIFFRACTION99.97

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