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- PDB-5o8y: Conformational dynamism for DNA interaction in Salmonella typhimu... -

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Basic information

Entry
Database: PDB / ID: 5o8y
TitleConformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.
ComponentsTranscriptional regulatory protein RcsB
KeywordsTRANSCRIPTION / Response regulator Transcriptional factor
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional regulatory protein RcsB / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain ...Transcriptional regulatory protein RcsB / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / 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
Transcriptional regulatory protein RcsB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCasino, P. / Marina, A. / Miguel-Romero, L. / Huesa, J.
Funding support Spain, 3items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBFU2016-78606-P Spain
Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
Ministry of Economy and CompetitivenessBIO2013-42619-P Spain
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Conformational dynamism for DNA interaction in the Salmonella RcsB response regulator.
Authors: Casino, P. / Miguel-Romero, L. / Huesa, J. / Garcia, P. / Garcia-Del Portillo, F. / Marina, A.
History
DepositionJun 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein RcsB
C: Transcriptional regulatory protein RcsB
D: Transcriptional regulatory protein RcsB
G: Transcriptional regulatory protein RcsB
F: Transcriptional regulatory protein RcsB
H: Transcriptional regulatory protein RcsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,13118
Polymers142,4626
Non-polymers1,67012
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, The dimer is supported by gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18380 Å2
ΔGint-204 kcal/mol
Surface area52540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.830, 108.830, 306.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Transcriptional regulatory protein RcsB


Mass: 23743.650 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: rcsB, STM2270 / Production host: Escherichia coli (E. coli) / References: UniProt: P58663
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.4M lithium sulfate 8% PEG1000 Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.256→102.6 Å / Num. obs: 87626 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.035 / Rrim(I) all: 0.179 / Net I/σ(I): 17.9
Reflection shellResolution: 2.256→2.264 Å / Redundancy: 1.7 % / Num. unique obs: 845 / Rpim(I) all: 0.652 / Rrim(I) all: 2.958 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A04

1a04


Resolution: 2.3→102.56 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.777 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25274 4145 5 %RANDOM
Rwork0.22335 ---
obs0.22484 78637 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.366 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 2.3→102.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9358 0 98 111 9567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199602
X-RAY DIFFRACTIONr_bond_other_d0.0010.029616
X-RAY DIFFRACTIONr_angle_refined_deg1.1862.00412996
X-RAY DIFFRACTIONr_angle_other_deg0.891322339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3751243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86525.505327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.947151761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9281532
X-RAY DIFFRACTIONr_chiral_restr0.0630.21589
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021656
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0915.0394966
X-RAY DIFFRACTIONr_mcbond_other2.095.0394965
X-RAY DIFFRACTIONr_mcangle_it3.4957.5496199
X-RAY DIFFRACTIONr_mcangle_other3.4947.556200
X-RAY DIFFRACTIONr_scbond_it2.4045.3584636
X-RAY DIFFRACTIONr_scbond_other2.3945.3424596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0797.8596734
X-RAY DIFFRACTIONr_long_range_B_refined6.25259.7879941
X-RAY DIFFRACTIONr_long_range_B_other6.22659.7659928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 346 -
Rwork0.269 5679 -
obs--100 %

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