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- PDB-6eo3: Conformational dynamism for DNA interaction in Salmonella typhimu... -

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Basic information

Entry
Database: PDB / ID: 6eo3
TitleConformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator. S207C P212121
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: 2.5 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 1.3Jan 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulatory protein RcsB
B: Transcriptional regulatory protein RcsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3944
Polymers46,2022
Non-polymers1922
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-37 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.621, 74.222, 75.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulatory protein RcsB


Mass: 23101.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The side chain for the following residues could not be traced, so they remain as Ala: N2, K127, E132, D148, K149, R150, R160, 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 16 % PEG4000, 0.2 M lithium sulfate and Tris pH 8.5

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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: 2.5→75.2 Å / Num. obs: 14033 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Rrim(I) all: 0.072 / Net I/σ(I): 17.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1541 / CC1/2: 0.817 / Rpim(I) all: 0.295 / Rrim(I) all: 0.718 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O8Y

5o8y


Resolution: 2.5→52.83 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 26.322 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 1.005 / ESU R Free: 0.33 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26898 701 5 %RANDOM
Rwork0.21513 ---
obs0.21795 13288 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---3.5 Å20 Å2
3---4 Å2
Refinement stepCycle: 1 / Resolution: 2.5→52.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 10 31 3092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193104
X-RAY DIFFRACTIONr_bond_other_d0.0050.023171
X-RAY DIFFRACTIONr_angle_refined_deg1.0982.0014204
X-RAY DIFFRACTIONr_angle_other_deg0.74437319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2325397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49626.055109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11815581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.071158
X-RAY DIFFRACTIONr_chiral_restr0.0590.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213393
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
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_it1.974.4911600
X-RAY DIFFRACTIONr_mcbond_other1.9664.491599
X-RAY DIFFRACTIONr_mcangle_it3.2456.721993
X-RAY DIFFRACTIONr_mcangle_other3.2446.7211994
X-RAY DIFFRACTIONr_scbond_it1.924.7041504
X-RAY DIFFRACTIONr_scbond_other1.8974.6871495
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1976.9242199
X-RAY DIFFRACTIONr_long_range_B_refined5.45535.2313345
X-RAY DIFFRACTIONr_long_range_B_other5.45635.2393345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 23 -
Rwork0.27 972 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5025-0.26860.0891.62890.18461.73370.21290.158-0.05150.0993-0.0214-0.0530.00620.0309-0.19150.04410.0323-0.01860.16040.01780.122911.5804-18.398236.8912
22.6772-0.0392-4.45490.33780.50558.0347-0.04210.16620.16170.0164-0.13040.32820.1772-0.44330.17250.1623-0.00510.03220.0994-0.10310.3396-10.3868-26.647829.6896
33.84210.75750.09816.58883.02511.8628-0.0317-0.1532-0.10370.0838-0.2140.19120.1116-0.22750.24570.0228-0.02430.0370.1151-0.01990.0819-17.9742-30.03013.9974
44.74570.62480.5082.1274-0.55710.54240.22730.14690.0950.0927-0.1060.08010.00620.0794-0.12120.0716-0.01380.03470.12240.0040.06418.9889-36.6282-10.9428
514.38774.9944-6.81181.8-2.64724.7189-0.23720.4480.1092-0.08840.15710.0316-0.0379-0.34880.08010.11180.0691-0.06770.13370.01920.1043-5.4219-26.4475-16.2568
62.81146.74021.711516.28264.60653.10180.1218-0.0397-0.01630.1486-0.1594-0.0329-0.509-0.27880.03760.17830.0656-0.00460.05490.01860.0592-10.7835-21.726-7.3263
71.76180.08670.94543.39731.61935.1081-0.1433-0.24760.1029-0.22020.05840.1648-0.20380.30960.08490.03050.0221-0.02350.19470.02290.0436-3.6463-9.545117.0026
84.2478-0.9244-0.0141.931-1.45435.84040.20960.0917-0.22190.03460.03820.14690.4447-0.2548-0.24770.0769-0.0308-0.04040.08980.02420.0795-0.1253-24.080134.8912
94.7714-2.395-2.61711.52630.98991.80810.32560.3870.3492-0.1743-0.075-0.0419-0.1198-0.3098-0.25060.12890.04020.06150.18030.11150.1896-2.2788-30.0669-10.516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 87
2X-RAY DIFFRACTION2A133 - 141
3X-RAY DIFFRACTION3A150 - 207
4X-RAY DIFFRACTION4B3 - 87
5X-RAY DIFFRACTION5B126 - 132
6X-RAY DIFFRACTION6B133 - 140
7X-RAY DIFFRACTION7B150 - 207
8X-RAY DIFFRACTION8A88 - 125
9X-RAY DIFFRACTION9B88 - 125

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