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- PDB-2zhg: Crystal structure of SoxR in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 2zhg
TitleCrystal structure of SoxR in complex with DNA
Components
  • DNA (5'-D(*DGP*DCP*DCP*DTP*DCP*DAP*DAP*DGP*DTP*DTP*DAP*DAP*DCP*DTP*DTP*DGP*DAP*DGP*DGP*DC)-3')
  • Redox-sensitive transcriptional activator soxR
KeywordsTRANSCRIPTION/DNA / oxidative stress / MerR family / Activator / DNA-binding / Iron / Iron-sulfur / Metal-binding / Transcription / Transcription regulation / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / response to oxidative stress / DNA-binding transcription factor activity / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
Redox-sensitive transcriptional activator SoxR / Transcription regulator MerR, DNA binding / MerR, DNA binding / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / MerR-type HTH domain signature. / : / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance ...Redox-sensitive transcriptional activator SoxR / Transcription regulator MerR, DNA binding / MerR, DNA binding / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / MerR-type HTH domain signature. / : / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / FE2/S2 (INORGANIC) CLUSTER / DNA / DNA (> 10) / Redox-sensitive transcriptional activator SoxR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsWatanabe, S. / Kita, A. / Kobayashi, K. / Miki, K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA
Authors: Watanabe, S. / Kita, A. / Kobayashi, K. / Miki, K.
History
DepositionFeb 5, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA (5'-D(*DGP*DCP*DCP*DTP*DCP*DAP*DAP*DGP*DTP*DTP*DAP*DAP*DCP*DTP*DTP*DGP*DAP*DGP*DGP*DC)-3')
A: Redox-sensitive transcriptional activator soxR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7345
Polymers23,3122
Non-polymers4223
Water39622
1
B: DNA (5'-D(*DGP*DCP*DCP*DTP*DCP*DAP*DAP*DGP*DTP*DTP*DAP*DAP*DCP*DTP*DTP*DGP*DAP*DGP*DGP*DC)-3')
A: Redox-sensitive transcriptional activator soxR
hetero molecules

B: DNA (5'-D(*DGP*DCP*DCP*DTP*DCP*DAP*DAP*DGP*DTP*DTP*DAP*DAP*DCP*DTP*DTP*DGP*DAP*DGP*DGP*DC)-3')
A: Redox-sensitive transcriptional activator soxR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,46810
Polymers46,6234
Non-polymers8446
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area9090 Å2
ΔGint-85.2 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.374, 53.374, 355.159
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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DNA chain / Protein , 2 types, 2 molecules BA

#1: DNA chain DNA (5'-D(*DGP*DCP*DCP*DTP*DCP*DAP*DAP*DGP*DTP*DTP*DAP*DAP*DCP*DTP*DTP*DGP*DAP*DGP*DGP*DC)-3')


Mass: 6133.979 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Redox-sensitive transcriptional activator soxR


Mass: 17177.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: soxR / Plasmid: pET-3Xa / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACS2

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Non-polymers , 4 types, 25 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 8

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 50mM Bis-Tris pH 6.6-6.8, 0.3M K/Na tartrate, 15% (w/v) PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Bis-TrisBis-tris methane11
2K/Na tartrate11
3PEG 1000011
4HOH11
5Bis-TrisBis-tris methane12
6K/Na tartrate12
7PEG 1000012
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 7602 / Num. obs: 7602 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.93 Å / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.6 / % possible all: 58.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.94 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1347236.98 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 455 6.1 %RANDOM
Rwork0.243 ---
obs0.243 7518 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.5842 Å2 / ksol: 0.304542 e/Å3
Displacement parametersBiso mean: 84.4 Å2
Baniso -1Baniso -2Baniso -3
1-21.81 Å223.1 Å20 Å2
2--21.81 Å20 Å2
3----43.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.78 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 407 18 22 1361
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.31
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it9.921.5
X-RAY DIFFRACTIONc_mcangle_it10.052
X-RAY DIFFRACTIONc_scbond_it8.592
X-RAY DIFFRACTIONc_scangle_it10.552.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.471 51 6.5 %
Rwork0.451 729 -
obs--59.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION4li4.paramli4.top
X-RAY DIFFRACTION5fes.par5fes.top2

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