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- PDB-8ad6: Structure of DarB bound to c-di-AMP -

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Basic information

Entry
Database: PDB / ID: 8ad6
TitleStructure of DarB bound to c-di-AMP
ComponentsCBS domain-containing protein
KeywordsSIGNALING PROTEIN / c-di-AMP / potassium stress / ppGpp / Rel / stringent factor / CbpB
Function / homologyCBS domain superfamily / Chem-2BA / CBS domain-containing protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsGarcia-Pino, A. / Talavera, A.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)T.0066.18 Belgium
CitationJournal: To Be Published
Title: Structure of DarB bound to c-di-AMP
Authors: Garcia-Pino, A. / Talavera, A.
History
DepositionJul 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: CBS domain-containing protein
B: CBS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6244
Polymers33,3072
Non-polymers1,3172
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-22 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.617, 42.293, 64.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein CBS domain-containing protein / Inosine-5'-monophosphate dehydrogenase


Mass: 16653.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3749, Bateq7PJ16_1575, C6Y43_13715, FAL52_03995
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A164SLA6
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293.16 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Lithium sulfate 0.1 M MES 6.0 20 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.52→52.81 Å / Num. obs: 40317 / % possible obs: 88 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 19.2
Reflection shellResolution: 1.52→1.57 Å / Num. unique obs: 998 / CC1/2: 0.826 / Rpim(I) all: 0.251

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YJ8

6yj8


Resolution: 1.52→52.81 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194 --
Rwork0.174 --
obs-40317 88 %
Displacement parametersBiso mean: 22.73 Å2
Refinement stepCycle: LAST / Resolution: 1.52→52.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 88 271 2515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632332
X-RAY DIFFRACTIONf_angle_d0.92153185
X-RAY DIFFRACTIONf_chiral_restr0.0636377
X-RAY DIFFRACTIONf_plane_restr0.0055451
X-RAY DIFFRACTIONf_dihedral_angle_d16.7727918

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