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- PDB-5o8z: Conformational dynamism for DNA interaction in Salmonella typhimu... -

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Basic information

Entry
Database: PDB / ID: 5o8z
TitleConformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.
ComponentsTranscriptional regulatory protein RcsB
KeywordsTRANSCRIPTION / Response regulator 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 / Transcriptional regulatory protein RcsB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCasino, P. / Marina, A. / Miguel-Romero, L. / Huesa, J.
Funding support Spain, 3items
OrganizationGrant numberCountry
Ministry of Economy and CompetitivenessBFU2016-78606-P Spain
Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
Ministry of Economy and CompetitivenessBIO2013-42619-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
DepositionJun 14, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)47,6686
Polymers47,4872
Non-polymers1814
Water1,58588
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-38 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.392, 54.266, 54.986
Angle α, β, γ (deg.)62.60, 81.61, 79.66
Int Tables number1
Space group name H-MP1

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Components

#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 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: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 29% Jeffamine ED2003 0.1M lithium sulfate Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.1→48.69 Å / Num. obs: 21487 / % possible obs: 97.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Net I/σ(I): 16.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.851 / Num. unique obs: 1736 / Rpim(I) all: 0.37 / Rrim(I) all: 1.004 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A04

1a04


Resolution: 2.1→48.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.275 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.224 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26542 1026 4.8 %RANDOM
Rwork0.21303 ---
obs0.21545 20461 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.953 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å2-0.12 Å21.29 Å2
2--0.9 Å2-0.3 Å2
3---0.68 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 10 88 3143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193112
X-RAY DIFFRACTIONr_bond_other_d0.0020.023123
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9954223
X-RAY DIFFRACTIONr_angle_other_deg0.93637244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4275411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04925.673104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58315560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2841510
X-RAY DIFFRACTIONr_chiral_restr0.0720.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
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_it1.2983.3271638
X-RAY DIFFRACTIONr_mcbond_other1.2943.3241637
X-RAY DIFFRACTIONr_mcangle_it2.2744.9682042
X-RAY DIFFRACTIONr_mcangle_other2.2744.9722043
X-RAY DIFFRACTIONr_scbond_it1.0713.3961474
X-RAY DIFFRACTIONr_scbond_other1.0723.4021469
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8635.0432173
X-RAY DIFFRACTIONr_long_range_B_refined4.32139.6763328
X-RAY DIFFRACTIONr_long_range_B_other4.30339.6333321
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 75 -
Rwork0.287 1484 -
obs--96.41 %
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)
12.5526-0.3462-0.82352.30420.09233.5635-0.04620.04460.0676-0.27330.078-0.16790.07430.007-0.03180.0467-0.0230.02660.0262-0.03840.0926-0.71581.2356-0.3867
26.7746-1.9453-0.93359.00491.36930.273-0.03980.31990.1233-0.30310.02430.2219-0.035-0.04090.01550.13380.0058-0.05330.2254-0.02130.0717-13.98986.6544-8.6616
36.73960.1994-1.61781.6392-1.13042.1752-0.4206-0.13661.11750.35710.2704-0.206-0.3713-0.09730.15020.49370.0117-0.06010.0864-0.09770.3583-5.211523.08049.0889
42.9421-0.99520.30972.8591-0.19523.1075-0.0811-0.2315-0.2998-0.0360.19250.18610.2294-0.2095-0.11140.0259-0.0148-0.00930.04240.03030.1045-16.0728-5.48220.7179
52.8167-0.8837-1.55068.52636.08317.2552-0.0545-0.22380.45160.184-0.0942-0.7263-0.1330.24820.14870.0413-0.0106-0.10960.1643-0.00710.3808-2.23824.724929.2757
61.8996-2.3516-0.21275.44430.84721.89220.21740.15010.3822-0.21220.0267-0.0253-0.3593-0.031-0.24420.23930.05360.09180.10430.03180.2411-19.406624.070326.0564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 124
2X-RAY DIFFRACTION2A131 - 140
3X-RAY DIFFRACTION3A153 - 207
4X-RAY DIFFRACTION4B2 - 124
5X-RAY DIFFRACTION5B130 - 141
6X-RAY DIFFRACTION6B153 - 207

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