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- PDB-8ogq: PanDDA analysis group deposition -- CdaA in complex with fragment... -

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Basic information

Entry
Database: PDB / ID: 8ogq
TitlePanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry B06
ComponentsCyclic di-AMP synthase CdaA
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
(1S)-1-(4-nitrophenyl)ethan-1-ol / Cyclic di-AMP synthase CdaA
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsGarbers, T.B. / Neumann, P. / Wollenhaupt, J. / Weiss, M.S. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Crystallographic fragment screen of the c-di-AMP-synthesizing enzyme CdaA from Bacillus subtilis.
Authors: Garbers, T. / Neumann, P. / Wollenhaupt, J. / Dickmanns, A. / Weiss, M.S. / Ficner, R.
History
DepositionMar 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic di-AMP synthase CdaA
B: Cyclic di-AMP synthase CdaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5544
Polymers33,3622
Non-polymers1912
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-13 kcal/mol
Surface area14430 Å2
Unit cell
Length a, b, c (Å)119.270, 38.930, 68.120
Angle α, β, γ (deg.)90.000, 95.370, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 16681.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: cdaA, ybbP, BSU01750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45589, diadenylate cyclase
#2: Chemical ChemComp-R8P / (1S)-1-(4-nitrophenyl)ethan-1-ol


Mass: 167.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 0.1 M Magnesium chloride 30 % (v/v) PEG 400 20 % (v/v) DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 116915 / % possible obs: 97.2 % / Redundancy: 2.6 % / Biso Wilson estimate: 19.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.107 / Net I/σ(I): 6.04
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.4-1.442.45286130.233.0491
1.44-1.481.94284210.2662.4221
1.48-1.521.42681920.3691.7791
1.52-1.571.08680100.5111.3561
1.57-1.620.83875930.611.0541
1.62-1.670.66173970.7470.8281
1.67-1.740.54672850.830.6781
1.74-1.810.42769100.8660.5311
1.81-1.890.30567640.9140.3791
1.89-1.980.20563790.9610.2561
1.98-2.090.14259720.9780.181
2.09-2.210.11857860.9880.1471
2.21-2.370.09154280.9890.1131
2.37-2.560.07650070.9910.0941
2.56-2.80.06446510.9930.0811
2.8-3.130.04840270.9950.0611
3.13-3.610.04236930.9950.0531
3.61-4.430.03831090.9950.0481
4.43-6.260.03823400.9950.0481

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→32.88 Å / SU ML: 0.219 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2253 2098 3.58 %
Rwork0.1965 56438 -
obs0.1975 58536 97.99 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.55 Å2
Refinement stepCycle: LAST / Resolution: 1.42→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 13 110 2388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752353
X-RAY DIFFRACTIONf_angle_d0.99533194
X-RAY DIFFRACTIONf_chiral_restr0.0756389
X-RAY DIFFRACTIONf_plane_restr0.0078413
X-RAY DIFFRACTIONf_dihedral_angle_d6.853330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.49731250.44283405X-RAY DIFFRACTION88.87
1.45-1.480.34861390.3833718X-RAY DIFFRACTION98.17
1.48-1.520.371390.31483746X-RAY DIFFRACTION98.35
1.52-1.570.31621410.28593776X-RAY DIFFRACTION98.52
1.57-1.620.2741380.25533707X-RAY DIFFRACTION97.79
1.62-1.680.24861400.23553770X-RAY DIFFRACTION98.29
1.68-1.750.28881400.22443752X-RAY DIFFRACTION98.61
1.75-1.820.26111400.19963781X-RAY DIFFRACTION99.02
1.82-1.920.26531410.18083789X-RAY DIFFRACTION99.02
1.92-2.040.2071410.17243771X-RAY DIFFRACTION98.42
2.04-2.20.21381410.17213814X-RAY DIFFRACTION99.02
2.2-2.420.17431430.17193831X-RAY DIFFRACTION99.3
2.42-2.770.25041420.1843823X-RAY DIFFRACTION99.3
2.77-3.490.2071420.1953820X-RAY DIFFRACTION98.53
3.49-32.880.19391460.17833935X-RAY DIFFRACTION98.62

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