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- PDB-6zz9: Crystal structure of CbpB from Streptococcus agalactiae -

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Basic information

Entry
Database: PDB / ID: 6zz9
TitleCrystal structure of CbpB from Streptococcus agalactiae
ComponentsCBS domain-containing protein
KeywordsSIGNALING PROTEIN / CBS / c-di-AMP
Function / homology: / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / : / Cyclic-di-AMP-binding protein CbpB
Function and homology information
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.644 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 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)40,3757
Polymers39,6972
Non-polymers6785
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-122 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.61, 60.61, 190.47
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 19848.572 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 200 mM ammonium sulfate, 100 mM MES pH 6.5, 30% w/v PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0716 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 2.644→47.62 Å / Num. obs: 11037 / % possible obs: 98.94 % / Redundancy: 4.3 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.06712 / Rpim(I) all: 0.03644 / Rrim(I) all: 0.07653 / Net I/σ(I): 10.76
Reflection shellResolution: 2.644→2.739 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.346 / Num. unique obs: 1030 / CC1/2: 0.709 / CC star: 0.911 / Rpim(I) all: 0.7379 / Rrim(I) all: 1.538 / % possible all: 96.34

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
AutoSolphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.644→47.62 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 1.075 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.586 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.321
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 551 -RANDOM
Rwork0.2331 ---
obs0.2341 11003 99.2 %-
Displacement parametersBiso mean: 100.59 Å2
Baniso -1Baniso -2Baniso -3
1--13.357 Å20 Å20 Å2
2---13.357 Å20 Å2
3---26.714 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.644→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 17 0 2542
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072589HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.893518HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d895SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes429HARMONIC5
X-RAY DIFFRACTIONt_it2589HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion368SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1902SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion17.66
LS refinement shellResolution: 2.644→2.68 Å
RfactorNum. reflection% reflection
Rfree0.4351 21 -
Rwork0.3025 --
obs--92.69 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.824-0.4223-2.22730-1.10083.430.01140.1423-0.12840.14230.04630.1058-0.12840.1058-0.05770.1488-0.1475-0.083-0.0113-0.0151-0.027728.643833.6122.275
20.8777-0.77081.49680.6128-1.12792.443-0.031-0.09170.4106-0.09170.0426-0.08430.4106-0.0843-0.01160.1356-0.152-0.0636-0.12520.04460.00629.942325.600219.8683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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