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- PDB-6zil: Structure of the isolated REC domain of RcsB from Salmonella ente... -

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Basic information

Entry
Database: PDB / ID: 6zil
TitleStructure of the isolated REC domain of RcsB from Salmonella enterica serovar Typhimurium in the apo form
ComponentsTranscriptional 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 / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, 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 / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulatory protein RcsB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 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 1.2Jan 31, 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
B: Transcriptional regulatory protein RcsB


Theoretical massNumber of molelcules
Total (without water)15,7031
Polymers15,7031
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7020 Å2
Unit cell
Length a, b, c (Å)148.136, 148.136, 148.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Transcriptional regulatory protein RcsB


Mass: 15703.307 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.31 Å3/Da / Density % sol: 71.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1.6M Tartrate, 0.1 M Hepes pH 7.5 and glucose 2.85%

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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 S 6M / Detector: PIXEL / Date: Jun 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.12→104.75 Å / Num. obs: 5069 / % possible obs: 96.8 % / Redundancy: 34.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.009 / Rrim(I) all: 0.052 / Net I/σ(I): 36.7 / Num. measured all: 176922 / Scaling rejects: 35
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
3.12-3.42372.4474489312130.8150.4052.4812.2
7.64-104.7530.70.024127804160.9970.0050.024132.3

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Processing

Software
NameVersionClassification
Aimless0.2.8data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O8Z

5o8z


Resolution: 3.12→104.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 22.654 / SU ML: 0.387 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.968 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3018 496 9.9 %RANDOM
Rwork0.2558 ---
obs0.2599 4534 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 221.91 Å2 / Biso mean: 165.056 Å2 / Biso min: 116.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.12→104.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 0 1 955
Biso mean---143.22 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019969
X-RAY DIFFRACTIONr_bond_other_d0.0020.02999
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9841326
X-RAY DIFFRACTIONr_angle_other_deg0.85932291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54726.07128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28515150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.576151
X-RAY DIFFRACTIONr_chiral_restr0.0570.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02182
LS refinement shellResolution: 3.12→3.201 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 37 -
Rwork0.394 348 -
all-385 -
obs--99.48 %

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