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- PDB-1lq1: DNA Complexed Structure of the Key Transcription Factor Initiatin... -

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Basic information

Entry
Database: PDB / ID: 1lq1
TitleDNA Complexed Structure of the Key Transcription Factor Initiating Development in Sporulation Bacteria
Components
  • 5'-D(*AP*CP*AP*AP*AP*AP*TP*TP*CP*GP*AP*CP*AP*CP*GP*A)-3'
  • 5'-D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3'
  • Stage 0 sporulation protein A
KeywordsTRANSCRIPTION/DNA / Spo0A / transcriptional activation and repression / 0A box / DNA complexed structure / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


detection of stimulus / single-species surface biofilm formation / cell septum assembly / positive regulation of sporulation resulting in formation of a cellular spore / asymmetric cell division / sporulation resulting in formation of a cellular spore / phosphorelay signal transduction system / DNA-binding transcription factor activity / calcium ion binding / positive regulation of DNA-templated transcription ...detection of stimulus / single-species surface biofilm formation / cell septum assembly / positive regulation of sporulation resulting in formation of a cellular spore / asymmetric cell division / sporulation resulting in formation of a cellular spore / phosphorelay signal transduction system / DNA-binding transcription factor activity / calcium ion binding / positive regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Sporulation transcription factor Spo0A / Sporulation initiation factor Spo0A, C-terminal / Sporulation initiation factor Spo0A C terminal / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Sporulation transcription factor Spo0A / Sporulation initiation factor Spo0A, C-terminal / Sporulation initiation factor Spo0A C terminal / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Stage 0 sporulation protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsZhao, H. / Msadek, T. / Zapf, J. / Madhusudan / Hoch, J.A. / Varughese, K.I.
CitationJournal: Structure / Year: 2002
Title: DNA complexed structure of the key transcription factor initiating development in sporulating bacteria.
Authors: Zhao, H. / Msadek, T. / Zapf, J. / Madhusudan / Hoch, J.A. / Varughese, K.I.
History
DepositionMay 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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
E: 5'-D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3'
F: 5'-D(*AP*CP*AP*AP*AP*AP*TP*TP*CP*GP*AP*CP*AP*CP*GP*A)-3'
G: 5'-D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3'
H: 5'-D(*AP*CP*AP*AP*AP*AP*TP*TP*CP*GP*AP*CP*AP*CP*GP*A)-3'
A: Stage 0 sporulation protein A
B: Stage 0 sporulation protein A
C: Stage 0 sporulation protein A
D: Stage 0 sporulation protein A


Theoretical massNumber of molelcules
Total (without water)73,1798
Polymers73,1798
Non-polymers00
Water4,396244
1
E: 5'-D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3'
F: 5'-D(*AP*CP*AP*AP*AP*AP*TP*TP*CP*GP*AP*CP*AP*CP*GP*A)-3'
C: Stage 0 sporulation protein A
D: Stage 0 sporulation protein A


Theoretical massNumber of molelcules
Total (without water)36,5894
Polymers36,5894
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3'
H: 5'-D(*AP*CP*AP*AP*AP*AP*TP*TP*CP*GP*AP*CP*AP*CP*GP*A)-3'
A: Stage 0 sporulation protein A
B: Stage 0 sporulation protein A


Theoretical massNumber of molelcules
Total (without water)36,5894
Polymers36,5894
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.917, 83.301, 91.241
Angle α, β, γ (deg.)90.00, 94.18, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the tandem dimer between two Spo0AC.

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Components

#1: DNA chain 5'-D(*TP*TP*CP*GP*TP*GP*TP*CP*GP*AP*AP*TP*TP*TP*TP*G)-3'


Mass: 4910.185 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*CP*AP*AP*AP*AP*TP*TP*CP*GP*AP*CP*AP*CP*GP*A)-3'


Mass: 4884.222 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
Stage 0 sporulation protein A / Transcription factor Spo0A


Mass: 13397.535 Da / Num. of mol.: 4 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SPO0A / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06534
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.61 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: PEG3350, sodium chloride, calcium chloride, tris-HCl, iso-propanol, pH 7.0, VAPOR DIFFUSION, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG335011
2NaCl11
3CaCl11
4tris-HCl11
5iso-propanol11
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 %1drop
2100 mMTris-HCl1reservoirpH7.0
3100 mM1reservoirNaCl
42 mM1reservoirCaCl2
52 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 2001
Details: 58 cm long, Pt-coated, fused silica, vertical focus mirror; Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator
RadiationMonochromator: horizontal focus monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 37147 / % possible obs: 0.951 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Biso Wilson estimate: 44.144 Å2 / Rsym value: 0.055 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3377 / Rsym value: 0.646 / % possible all: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 32507 / % possible obs: 0.957 % / Num. measured all: 243795 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 78.2 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Isotropic thermal model: OVERALL ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1640 5 %RANDOM
Rwork0.217 ---
all0.23 33855 --
obs0.2185 32181 100 %-
Displacement parametersBiso mean: 65.2 Å2
Baniso -1Baniso -2Baniso -3
1-18.27 Å20 Å2-21.85 Å2
2---9.41 Å20 Å2
3----8.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 1300 0 244 4909
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_mcbond_it4.011.5
X-RAY DIFFRACTIONc_mcangle_it6.222
X-RAY DIFFRACTIONc_scbond_it5.822
X-RAY DIFFRACTIONc_scangle_it8.372.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 227 5 %
Rwork0.346 4279 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
Refinement
*PLUS
Rfactor all: 0.23 / Rfactor obs: 0.2185 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.409 / % reflection Rfree: 5 % / Rfactor Rwork: 0.346

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