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- PDB-6eo2: Conformational dynamism for DNA interaction in Salmonella typhimu... -

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Basic information

Entry
Database: PDB / ID: 6eo2
TitleConformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator. S207C crossed
ComponentsTranscriptional regulatory protein RcsB
KeywordsDNA BINDING PROTEIN / 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 enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCasino, P. / Marina, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-78606-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2013-42619-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2016-78571-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
DepositionOct 8, 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 / _citation_author.name
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 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)23,1011
Polymers23,1011
Non-polymers00
Water21612
1
A: Transcriptional regulatory protein RcsB

A: Transcriptional regulatory protein RcsB


Theoretical massNumber of molelcules
Total (without water)46,2022
Polymers46,2022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area3140 Å2
ΔGint-14 kcal/mol
Surface area19750 Å2
MethodPISA
2
A: Transcriptional regulatory protein RcsB
x 6


Theoretical massNumber of molelcules
Total (without water)138,6066
Polymers138,6066
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_564x,x-y+1,-z-1/21
Buried area14760 Å2
ΔGint-55 kcal/mol
Surface area53910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.952, 92.952, 120.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Transcriptional regulatory protein RcsB


Mass: 23101.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Some side chains could not be traced, thus, they remain at Ala at residues: M1, E28, E139, K140, I141, S142, D148, K149, R150, K180, V208.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: rcsB, STM2270 / Production host: Escherichia coli (E. coli) / References: UniProt: P58663
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 30 % polyacrylate 2100, 0.1 M sodium malonate and 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.6→80.6 Å / Num. obs: 195331 / % possible obs: 96.4 % / Redundancy: 20.2 % / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 31.8
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 17.8 % / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 17096 / Num. unique all: 958 / CC1/2: 0.826 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→80.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.95 / SU B: 11.248 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.436 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24587 491 5.1 %RANDOM
Rwork0.21914 ---
obs0.22059 9177 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å20 Å2
3----2.19 Å2
Refinement stepCycle: 1 / Resolution: 2.6→80.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 0 12 1578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191589
X-RAY DIFFRACTIONr_bond_other_d0.0010.021621
X-RAY DIFFRACTIONr_angle_refined_deg1.0181.9932153
X-RAY DIFFRACTIONr_angle_other_deg0.70533736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26725.71456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04615290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.723155
X-RAY DIFFRACTIONr_chiral_restr0.0560.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02314
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_it3.3997.749831
X-RAY DIFFRACTIONr_mcbond_other3.47.746830
X-RAY DIFFRACTIONr_mcangle_it5.42911.6231037
X-RAY DIFFRACTIONr_mcangle_other5.42711.6261038
X-RAY DIFFRACTIONr_scbond_it3.6037.933756
X-RAY DIFFRACTIONr_scbond_other3.6017.934757
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.94211.7571117
X-RAY DIFFRACTIONr_long_range_B_refined8.64259.691721
X-RAY DIFFRACTIONr_long_range_B_other8.64259.7091721
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 36 -
Rwork0.341 630 -
obs--91.86 %

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