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- PDB-1fc3: THE CRYSTAL STRUCTURE OF TRANS-ACTIVATION DOMAIN OF THE SPORULATI... -

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Basic information

Entry
Database: PDB / ID: 1fc3
TitleTHE CRYSTAL STRUCTURE OF TRANS-ACTIVATION DOMAIN OF THE SPORULATION RESPONSE REGULATOR, SPO0A
ComponentsSPO0A
KeywordsSIGNALING PROTEIN / RESPONSE REGULATOR
Function / homology
Function and homology information


detection of stimulus / regulation of sporulation resulting in formation of a cellular spore / sporulation resulting in formation of a cellular spore / phosphorelay signal transduction system / DNA-binding transcription factor activity / calcium ion binding / 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 ...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
Stage 0 sporulation protein A
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLewis, R.J. / Krzywda, S. / Wilkinson, A.J.
Citation
Journal: Mol.Microbiol. / Year: 2000
Title: The trans-activation domain of the sporulation response regulator Spo0A revealed by X-ray crystallography.
Authors: Lewis, R.J. / Krzywda, S. / Brannigan, J.A. / Turkenburg, J.P. / Muchova, K. / Dodson, E.J. / Barak, I. / Wilkinson, A.J.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Domain-Swapping in the Sporulation Response Regulator Spo0A
Authors: Lewis, R.J. / Muchova, K. / Brannigan, J.A. / Barak, I. / Leonard, G. / Wilkinson, A.J.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Phosphorylated Aspartate in the Structure of a Response Regulator Protein
Authors: Lewis, R.J. / Brannigan, J.A. / Muchova, K. / Barak, I. / Wilkinson, A.J.
History
DepositionJul 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

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Assembly

Deposited unit
A: SPO0A
B: SPO0A
C: SPO0A


Theoretical massNumber of molelcules
Total (without water)40,1233
Polymers40,1233
Non-polymers00
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.118, 53.414, 53.718
Angle α, β, γ (deg.)90.82, 111.73, 111.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein SPO0A / SPORULATION RESPONSE REGULATOR


Mass: 13374.438 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P52934
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.63 Å3/Da / Density % sol: 52.91 %
Crystal growpH: 7.5
Details: 0.1 M HEPES pH 7.5, 20% w/v PEG 10K, 0.1 M MALTOSE, 10 mM BME
Crystal
*PLUS
Density % sol: 53.4 %
Crystal grow
*PLUS
Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: Muchova, K., (1999) Acta Crystallogr., D55, 671.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1drop
31 mMdithiothreitol1drop
410 %(w/v)PEG40001reservoir
550 mM1reservoirLi2SO4
650 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 27976 / % possible obs: 87.6 % / Redundancy: 7.27 % / Biso Wilson estimate: 29.38 Å2 / Rsym value: 0.06 / Net I/σ(I): 19.41
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.31 % / Mean I/σ(I) obs: 3.23 / Rsym value: 0.313 / % possible all: 55.6
Reflection
*PLUS
Redundancy: 3.6 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 55.6 % / Rmerge(I) obs: 0.313

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Processing

Software
NameClassification
SOLVEphasing
DMmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / SU B: 5.00384 / SU ML: 0.13869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21172 / ESU R Free: 0.19734
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1221 5 %RANDOM
Rwork0.196 ---
obs0.1991 24473 87.6 %-
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0.44 Å2-1.64 Å2
2---1.36 Å2-0.95 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 0 319 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.541.5
X-RAY DIFFRACTIONp_mcangle_it0.9732
X-RAY DIFFRACTIONp_scbond_it1.4133
X-RAY DIFFRACTIONp_scangle_it2.0624.5
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.1420.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.9

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