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- PDB-6zza: Crystal structure of CbpB in complex with c-di-AMP -

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Basic information

Entry
Database: PDB / ID: 6zza
TitleCrystal structure of CbpB in complex with c-di-AMP
ComponentsCBS domain-containing protein
KeywordsSIGNALING PROTEIN / CBS / c-di-AMP
Function / homology: / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Chem-2BA / Cyclic-di-AMP-binding protein CbpB
Function and homology information
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.491 Å
AuthorsMechaly, A.E. / Covaleda-Cortes, G. / Kaminski, P.A.
CitationJournal: Febs J. / Year: 2023
Title: The c-di-AMP-binding protein CbpB modulates the level of ppGpp alarmone in Streptococcus agalactiae.
Authors: Covaleda-Cortes, G. / Mechaly, A. / Brissac, T. / Baehre, H. / Devaux, L. / England, P. / Raynal, B. / Hoos, S. / Gominet, M. / Firon, A. / Trieu-Cuot, P. / Kaminski, P.A.
History
DepositionAug 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Aug 13, 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_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

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Assembly

Deposited unit
A: CBS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6033
Polymers19,8491
Non-polymers7542
Water86548
1
A: CBS domain-containing protein
hetero molecules

A: CBS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2066
Polymers39,6972
Non-polymers1,5094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area2700 Å2
ΔGint-43 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.830, 93.830, 33.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein CBS domain-containing protein / FIG042801: CBS domain containing protein


Mass: 19848.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria)
Gene: ykuL, C6N06_01440, D5F95_08070, DX05_08405, E8E04_03435, F5F86_02645, NCTC9828_00932, WA02_02795, WA05_04310
Production host: Escherichia coli (E. coli) / References: UniProt: A0A076YWK5
#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.: 1 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 200 mM ammonium sulfate, 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 EIGER2 X 9M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.491→31.05 Å / Num. obs: 6110 / % possible obs: 99.12 % / Redundancy: 5.3 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1012 / Rpim(I) all: 0.04755 / Rrim(I) all: 0.1124 / Net I/σ(I): 9.79
Reflection shellResolution: 2.491→2.58 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.6201 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 578 / CC1/2: 0.798 / CC star: 0.942 / Rpim(I) all: 0.2914 / Rrim(I) all: 0.6887 / % possible all: 93.21

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Processing

Software
NameClassification
BUSTERrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZZ9

6zz9


Resolution: 2.491→31.05 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245 --
Rwork0.186 --
obs0.189 6101 99.1 %
Displacement parametersBiso mean: 67.54 Å2
Refinement stepCycle: LAST / Resolution: 2.491→31.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 49 48 1288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411269
X-RAY DIFFRACTIONf_angle_d1.74961733
X-RAY DIFFRACTIONf_chiral_restr0.1015205
X-RAY DIFFRACTIONf_plane_restr0.0064238
X-RAY DIFFRACTIONf_dihedral_angle_d21.6535484
LS refinement shellResolution: 2.491→2.78 Å
RfactorNum. reflection% reflection
Rfree0.3037 --
Rwork0.2115 1685 -
obs--96.95 %

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