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- PDB-6zj2: Structure of RcsB from Salmonella enterica serovar Typhimurium bo... -

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Basic information

Entry
Database: PDB / ID: 6zj2
TitleStructure of RcsB from Salmonella enterica serovar Typhimurium bound to promoter rprA in the presence of phosphomimetic BeF3-
Components
  • DNA (5'-D(P*CP*CP*GP*AP*TP*CP*AP*GP*AP*TP*TP*CP*GP*TP*CP*TP*CP*AP*AP*TP*AP*GP*G)-3')
  • Transcriptional regulatory protein RcsB
  • rprA promoter sequence
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 str. LT2 (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 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 27, 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 / 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_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_scientific_name / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _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
D: Transcriptional regulatory protein RcsB
C: Transcriptional regulatory protein RcsB
E: rprA promoter sequence
F: DNA (5'-D(P*CP*CP*GP*AP*TP*CP*AP*GP*AP*TP*TP*CP*GP*TP*CP*TP*CP*AP*AP*TP*AP*GP*G)-3')
G: rprA promoter sequence
I: DNA (5'-D(P*CP*CP*GP*AP*TP*CP*AP*GP*AP*TP*TP*CP*GP*TP*CP*TP*CP*AP*AP*TP*AP*GP*G)-3')
L: Transcriptional regulatory protein RcsB
M: Transcriptional regulatory protein RcsB
N: Transcriptional regulatory protein RcsB
O: Transcriptional regulatory protein RcsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,42118
Polymers218,19112
Non-polymers2296
Water00
1
B: Transcriptional regulatory protein RcsB
A: Transcriptional regulatory protein RcsB
G: rprA promoter sequence
I: DNA (5'-D(P*CP*CP*GP*AP*TP*CP*AP*GP*AP*TP*TP*CP*GP*TP*CP*TP*CP*AP*AP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7898
Polymers61,6084
Non-polymers1814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Transcriptional regulatory protein RcsB
C: Transcriptional regulatory protein RcsB
E: rprA promoter sequence
F: DNA (5'-D(P*CP*CP*GP*AP*TP*CP*AP*GP*AP*TP*TP*CP*GP*TP*CP*TP*CP*AP*AP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6576
Polymers61,6084
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
L: Transcriptional regulatory protein RcsB
M: Transcriptional regulatory protein RcsB
N: Transcriptional regulatory protein RcsB
O: Transcriptional regulatory protein RcsB


Theoretical massNumber of molelcules
Total (without water)94,9754
Polymers94,9754
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.356, 111.514, 146.262
Angle α, β, γ (deg.)90.000, 90.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcriptional regulatory protein RcsB


Mass: 23743.650 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: rcsB, STM2270 / Production host: Escherichia coli (E. coli) / References: UniProt: P58663
#2: DNA chain rprA promoter sequence


Mass: 7080.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*CP*CP*GP*AP*TP*CP*AP*GP*AP*TP*TP*CP*GP*TP*CP*TP*CP*AP*AP*TP*AP*GP*G)-3')


Mass: 7040.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 8000, MES pH 6.5 and 0.2M NaAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.38→45.99 Å / Num. obs: 30572 / % possible obs: 99.1 % / Redundancy: 3.8 % / CC1/2: 0.983 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.133 / Rrim(I) all: 0.266 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.4-3.580.6541580743820.7570.3980.7711.997.8
10.75-45.990.12362210090.9890.0690.1397.998.3

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O8Z

5o8z


Resolution: 3.38→45.99 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.829 / SU B: 22.271 / SU ML: 0.389 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3186 1581 5.2 %RANDOM
Rwork0.2655 ---
obs0.2681 28985 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 195.64 Å2 / Biso mean: 85.244 Å2 / Biso min: 35.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å26.72 Å2
2---54.67 Å2-0 Å2
3---55.26 Å2
Refinement stepCycle: final / Resolution: 3.38→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10265 1804 12 0 12081
Biso mean--69.19 --
Num. residues----1543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01312428
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711154
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.53117356
X-RAY DIFFRACTIONr_angle_other_deg1.0891.69325838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42651439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47726.185346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.432151545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3351513
X-RAY DIFFRACTIONr_chiral_restr0.0360.21833
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022185
LS refinement shellResolution: 3.38→3.468 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 74 -
Rwork0.257 1690 -
all-1764 -
obs--75.87 %

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