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- PDB-6zix: Structure of RcsB from Salmonella enterica serovar Typhimurium bo... -

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Basic information

Entry
Database: PDB / ID: 6zix
TitleStructure of RcsB from Salmonella enterica serovar Typhimurium bound to promoter P1flhDC in the presence of phosphomimetic BeF3-
Components
  • (P1flhDC promoter sequence of 23 ...) x 2
  • Transcriptional regulatory protein RcsB
KeywordsDNA BINDING PROTEIN / response regulator / phosphorylation / two-component systems / 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
BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / Transcriptional regulatory protein RcsB
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHuesa, J. / Marina, A. / Casino, P.
Funding support Spain, 4items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-78606-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2016-77639-P Spain
Spanish Ministry of Economy and CompetitivenessRYC-2014-16490 Spain
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon.
Authors: Huesa, J. / Giner-Lamia, J. / Pucciarelli, M.G. / Paredes-Martinez, F. / Portillo, F.G. / Marina, A. / Casino, P.
History
DepositionJun 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Jan 31, 2024Group: 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
B: Transcriptional regulatory protein RcsB
A: Transcriptional regulatory protein RcsB
E: P1flhDC promoter sequence of 23 bp
F: P1flhDC promoter sequence of 23 bp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7878
Polymers61,6064
Non-polymers1814
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Phosphorylated RcsB binds to DNA as EMSA experiments demonstrate
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-85 kcal/mol
Surface area24440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.220, 183.220, 84.143
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Transcriptional regulatory protein RcsB


Mass: 23743.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: rcsB, STM2270 / Production host: Escherichia coli (E. coli) / References: UniProt: P58663

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P1flhDC promoter sequence of 23 ... , 2 types, 2 molecules EF

#2: DNA chain P1flhDC promoter sequence of 23 bp


Mass: 7137.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A double-stranded DNA chain E: CGAATTAGGAAAAATCTTAGGCG chain F: GCTTAATCCTTTTTAGAATCCGC
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli)
#3: DNA chain P1flhDC promoter sequence of 23 bp


Mass: 6981.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A double-stranded DNA chain E: CGAATTAGGAAAAATCTTAGGCG chain F: GCTTAATCCTTTTTAGAATCCGC
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 9 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.41 Å3/Da / Density % sol: 72.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1.5M ammonium sulfate, 1.6% glycerol and 0.8M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→74.34 Å / Num. obs: 14477 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Net I/σ(I): 11.8 / Num. measured all: 69020
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.4-3.674.80.4731447329990.9630.2410.5323.199.9
9-74.344.50.03535127880.9960.0180.03935.899.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O8Z

5o8z


Resolution: 3.4→57.79 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.959 / SU B: 77.191 / SU ML: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 694 4.8 %RANDOM
Rwork0.2389 ---
obs0.2407 13780 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 296.75 Å2 / Biso mean: 169.022 Å2 / Biso min: 73.91 Å2
Baniso -1Baniso -2Baniso -3
1--14.12 Å2-7.06 Å20 Å2
2---14.12 Å20 Å2
3---45.79 Å2
Refinement stepCycle: final / Resolution: 3.4→57.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 902 10 5 3753
Biso mean--172.95 86.73 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123887
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173309
X-RAY DIFFRACTIONr_angle_refined_deg1.21.4865489
X-RAY DIFFRACTIONr_angle_other_deg1.1321.7837676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.78826.48491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77315424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.768153
X-RAY DIFFRACTIONr_chiral_restr0.0440.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023783
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
LS refinement shellResolution: 3.4→3.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.551 47 -
Rwork0.512 1030 -
all-1077 -
obs--99.72 %

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