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- PDB-3qq6: The N-terminal DNA binding domain of SinR from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 3qq6
TitleThe N-terminal DNA binding domain of SinR from Bacillus subtilis
ComponentsHTH-type transcriptional regulator sinR
KeywordsTRANSCRIPTION / Helix-Turn-Helix motif / biofilm / repressor / transcriptional regulator / SinI
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
SinR repressor/SinI anti-repressor, dimerisation domain / SinR repressor/SinI anti-repressor, dimerisation domain superfamily / Anti-repressor SinI / Sin domain profile. / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...SinR repressor/SinI anti-repressor, dimerisation domain / SinR repressor/SinI anti-repressor, dimerisation domain superfamily / Anti-repressor SinI / Sin domain profile. / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator SinR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsColledge, V. / Fogg, M.J. / Levdikov, V.M. / Dodson, E.J. / Wilkinson, A.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure and Organisation of SinR, the Master Regulator of Biofilm Formation in Bacillus subtilis.
Authors: Colledge, V.L. / Fogg, M.J. / Levdikov, V.M. / Leech, A. / Dodson, E.J. / Wilkinson, A.J.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator sinR
B: HTH-type transcriptional regulator sinR


Theoretical massNumber of molelcules
Total (without water)17,8162
Polymers17,8162
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-4 kcal/mol
Surface area7070 Å2
2
A: HTH-type transcriptional regulator sinR


Theoretical massNumber of molelcules
Total (without water)8,9081
Polymers8,9081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: HTH-type transcriptional regulator sinR


Theoretical massNumber of molelcules
Total (without water)8,9081
Polymers8,9081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.970, 45.329, 85.244
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 HTH-type transcriptional regulator sinR


Mass: 8907.995 Da / Num. of mol.: 2 / Fragment: N-terminal domain of SinR residues 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU24610, flaD, sin, sinR / Plasmid: pET-YSBLIC- / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06533
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.9 Å3/Da / Density % sol: 35.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS pH 8.5, 27% PEG3350, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0039 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2007
RadiationMonochromator: channel-cut monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0039 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 10989 / Num. obs: 10989 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 4.87 / Num. unique all: 539 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0086refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B0N

1b0n


Resolution: 1.9→42.62 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.515 / SU ML: 0.134 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 524 4.8 %RANDOM
Rwork0.20364 ---
all0.20629 10411 --
obs0.20629 10411 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.434 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å20 Å20 Å2
2---2.34 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 0 67 1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211132
X-RAY DIFFRACTIONr_bond_other_d0.0010.02779
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9591522
X-RAY DIFFRACTIONr_angle_other_deg1.03931916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83724.42352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83415225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.579156
X-RAY DIFFRACTIONr_chiral_restr0.1230.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02212
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 23 -
Rwork0.245 727 -
obs--100 %

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