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- PDB-3gfi: Crystal structure of ST1710 complexed with its promoter DNA -

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Basic information

Entry
Database: PDB / ID: 3gfi
TitleCrystal structure of ST1710 complexed with its promoter DNA
Components
  • 146aa long hypothetical transcriptional regulator
  • 5'-D(*TP*AP*AP*CP*AP*AP*TP*AP*GP*CP*AP*AP*A)-3'
  • 5'-D(*TP*TP*GP*CP*TP*AP*TP*TP*GP*T)-3'
KeywordsTRANSCRIPTION/DNA / Transcription regulator / ST1710 / MarR / DNA-binding / Transcription / Transcription regulation / TRANSCRIPTION-DNA COMPLEX / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
MarR family / : / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / MarR family transcriptional regulator
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsKumarevel, T. / Tanaka, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: Nucleic Acids Res. / Year: 2009
Title: ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.
Authors: Kumarevel, T. / Tanaka, T. / Umehara, T. / Yokoyama, S.
#1: Journal: J.Struct.Biol. / Year: 2008
Title: Crystal structure of the MarR family regulatory protein, ST1710, from Sulfolobus tokodaii strain 7.
Authors: Kumarevel, T. / Tanaka, T. / Nishio, M. / Gopinath, S.C. / Takio, K. / Shinkai, A. / Kumar, P.K.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2013Group: Derived calculations
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 146aa long hypothetical transcriptional regulator
C: 146aa long hypothetical transcriptional regulator
D: 5'-D(*TP*AP*AP*CP*AP*AP*TP*AP*GP*CP*AP*AP*A)-3'
E: 5'-D(*TP*TP*GP*CP*TP*AP*TP*TP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)40,7774
Polymers40,7774
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.440, 106.730, 82.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 146aa long hypothetical transcriptional regulator / Transcription regulator ST1710


Mass: 16879.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Gene: ST1710 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CodonPlus (DE3)-RIL-X / References: UniProt: Q96ZY1
#2: DNA chain 5'-D(*TP*AP*AP*CP*AP*AP*TP*AP*GP*CP*AP*AP*A)-3'


Mass: 3976.652 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*TP*GP*CP*TP*AP*TP*TP*GP*T)-3'


Mass: 3041.000 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 30% 2-methyl-2,4-pentanediol (MPD) 0.02M Calcium chloride dehydrate, 0.1M sodium trihydrate, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Calcium chloride dehydrate11
3sodium trihydrate11
4MPD12
5Calcium chloride dehydrate12
6sodium trihydrate12

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97896, 0.97930, 1.000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 27, 2008
Details: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium
RadiationMonochromator: Fixed exit Si double crystal monochromator, Si (111)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.97931
311
ReflectionResolution: 2.1→40 Å / Num. all: 24231 / Num. obs: 24231 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.067
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9.8 % / Num. unique all: 2372 / Rsym value: 0.281 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementResolution: 2.1→19.75 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2021016.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1726 7.1 %RANDOM
Rwork0.234 ---
obs0.234 24202 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.2158 Å2 / ksol: 0.360857 e/Å3
Displacement parametersBiso max: 100.15 Å2 / Biso mean: 51.1 Å2 / Biso min: 18.15 Å2
Baniso -1Baniso -2Baniso -3
1--4.8 Å20 Å20 Å2
2---1.71 Å20 Å2
3---6.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 466 0 154 2925
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.372.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 262 6.8 %
Rwork0.242 3577 -
obs--94.9 %
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_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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