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- PDB-6wsh: Crystal structure of EutV from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 6wsh
TitleCrystal structure of EutV from Enterococcus faecalis
ComponentsResponse regulator
KeywordsRNA BINDING PROTEIN / RNA binding / ANTAR domain / antitermination
Function / homology
Function and homology information


phosphorelay signal transduction system / RNA binding
Similarity search - Function
Signal transduction response regulator, antiterminator / ANTAR domain / ANTAR domain / ANTAR domain profile. / ANTAR / : / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Signal transduction response regulator, antiterminator / ANTAR domain / ANTAR domain / ANTAR domain profile. / ANTAR / : / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsAtaide, S.F. / Walshe, J.L.
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural characterization of the ANTAR antiterminator domain bound to RNA.
Authors: Walshe, J.L. / Siddiquee, R. / Patel, K. / Ataide, S.F.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 26, 2022Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Oct 18, 2023Group: 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: Response regulator
B: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,45216
Polymers43,0582
Non-polymers39414
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-149 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.539, 85.688, 97.456
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 Response regulator


Mass: 21529.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria)
Gene: BZG32_08120, CUN08_06285, DVW78_01210, FKY84_00940, KUB3007_C13700
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q1FU69
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.075M Tris pH 8.5, 18-20% v/v tert-butanol, 25% v/v glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.12→42.85 Å / Num. obs: 26642 / % possible obs: 99.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 15.57 Å2 / CC1/2: 0.984 / Net I/σ(I): 6
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 2.9 % / Num. unique obs: 2134 / CC1/2: 0.377 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3758refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s8n, 1qo0

1s8n

1qo0


Resolution: 2.12→42.84 Å / SU ML: 0.2558 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2405 1232 4.64 %
Rwork0.2392 25345 -
obs0.2392 26577 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.97 Å2
Refinement stepCycle: LAST / Resolution: 2.12→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 19 120 3111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822999
X-RAY DIFFRACTIONf_angle_d1.21384025
X-RAY DIFFRACTIONf_chiral_restr0.0559484
X-RAY DIFFRACTIONf_plane_restr0.008512
X-RAY DIFFRACTIONf_dihedral_angle_d23.9231194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.20.31491360.31462749X-RAY DIFFRACTION100
2.2-2.310.32451520.28912766X-RAY DIFFRACTION100
2.31-2.430.26971060.28192806X-RAY DIFFRACTION100
2.43-2.580.27091370.25582777X-RAY DIFFRACTION100
2.58-2.780.25211520.24192776X-RAY DIFFRACTION99.97
2.78-3.060.26351180.24142828X-RAY DIFFRACTION99.9
3.06-3.50.2091200.22712830X-RAY DIFFRACTION99.93
3.5-4.410.21651630.20672824X-RAY DIFFRACTION99.83
4.41-42.840.1891480.20232989X-RAY DIFFRACTION99.84

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