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- PDB-6ww6: Crystal structure of EutV bound to RNA -

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Basic information

Entry
Database: PDB / ID: 6ww6
TitleCrystal structure of EutV bound to RNA
Components
  • Response regulator
  • eutP P2
KeywordsRNA BINDING PROTEIN/RNA / RNA binding / ANTAR domain / antitermination / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
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
BERYLLIUM TRIFLUORIDE ION / : / RNA / RNA (> 10) / Response regulator
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Response regulator
B: Response regulator
E: eutP P2
F: eutP P2
D: eutP P2
C: eutP P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2208
Polymers113,0886
Non-polymers1322
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)258.483, 258.483, 258.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Space group name HallI4bd2c3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y,-z+1/2,x
#11: z,-x,-y+1/2
#12: -y+1/2,z,-x
#13: -z,-x+1/2,y
#14: -z+1/2,x,-y
#15: y,-z,-x+1/2
#16: x,-y,-z+1/2
#17: -x+1/2,y,-z
#18: -x,-y+1/2,z
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x+1/2,y+1/2,z+1/2
#26: x+3/4,-z+3/4,y+5/4
#27: x+3/4,z+5/4,-y+5/4
#28: z+3/4,y+5/4,-x+5/4
#29: -z+3/4,y+5/4,x+3/4
#30: -y+3/4,x+5/4,z+3/4
#31: y+3/4,-x+3/4,z+5/4
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1,x+1/2
#35: z+1/2,-x+1/2,-y+1
#36: -y+1,z+1/2,-x+1/2
#37: -z+1/2,-x+1,y+1/2
#38: -z+1,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1
#40: x+1/2,-y+1/2,-z+1
#41: -x+1,y+1/2,-z+1/2
#42: -x+1/2,-y+1,z+1/2
#43: y+3/4,x+5/4,-z+5/4
#44: -y+3/4,-x+3/4,-z+3/4
#45: z+3/4,-y+3/4,x+5/4
#46: -z+3/4,-y+3/4,-x+3/4
#47: -x+3/4,z+5/4,y+3/4
#48: -x+3/4,-z+3/4,-y+3/4

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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
Details: Dimeric EutV bound simultaneously to two seperate dual hexaloops RNA molecules. Each EutV chain binds a single hexaloop from different RNA molecules with the 2nd hexaloop binding to the ...Details: Dimeric EutV bound simultaneously to two seperate dual hexaloops RNA molecules. Each EutV chain binds a single hexaloop from different RNA molecules with the 2nd hexaloop binding to the symmetry related EutV chain in a neighbouring ASUs
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: RNA chain
eutP P2


Mass: 17507.568 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Production host: Cloning vector pUC19 (others) / References: GenBank: 295112306
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Sodium chloride 0.1 M HEPES 1.4-1.8 M Ammonium sulfate

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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: Sep 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.8→47.19 Å / Num. obs: 14773 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 129.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.084 / Net I/σ(I): 9.1
Reflection shellResolution: 3.8→4.25 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4093 / CC1/2: 0.733 / Rpim(I) all: 0.489 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIXdev_3758refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WSH

6wsh


Resolution: 3.8→47.19 Å / SU ML: 0.4632 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9921
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2414 729 4.94 %
Rwork0.2331 14020 -
obs0.2336 14749 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 158.4 Å2
Refinement stepCycle: LAST / Resolution: 3.8→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 1484 8 0 4481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634678
X-RAY DIFFRACTIONf_angle_d0.95766631
X-RAY DIFFRACTIONf_chiral_restr0.0488831
X-RAY DIFFRACTIONf_plane_restr0.0067586
X-RAY DIFFRACTIONf_dihedral_angle_d18.32662016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.090.34841460.32152698X-RAY DIFFRACTION98.41
4.09-4.50.30511470.24962778X-RAY DIFFRACTION99.97
4.5-5.150.26071590.24132778X-RAY DIFFRACTION99.97
5.16-6.490.28661190.27292837X-RAY DIFFRACTION99.63
6.49-47.190.1831580.18932929X-RAY DIFFRACTION98.63

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