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- PDB-6swi: The C-terminal domain of AraT, a response regulator from Geobacil... -

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Basic information

Entry
Database: PDB / ID: 6swi
TitleThe C-terminal domain of AraT, a response regulator from Geobacillus stearothermophilus
ComponentsTwo-component response regulator
KeywordsTRANSCRIPTION / Response regulator / Geobacillus stearothermophilus / DNA binding / Arabinan utilization system
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
CdaR, GGDEF-like domain / : / GGDEF-like domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein ...CdaR, GGDEF-like domain / : / GGDEF-like domain / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
Two-component response regulator
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsLansky, S. / Lavid, N. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: The C-terminal domain of AraT, a response regulator from Geobacillus stearothermophilus
Authors: Lansky, S. / Lavid, N. / Shoham, Y. / Shoham, G.
History
DepositionSep 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)14,2711
Polymers14,2711
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.855, 38.744, 92.463
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Two-component response regulator


Mass: 14271.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: araT / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYL7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.69 Å3/Da / Density % sol: 27.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.95 M KNa-tartrate, 0.1 M Tris pH 8.5, and 0.5 % PEG MME 5K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 36653 / % possible obs: 98.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 35.1
Reflection shellResolution: 1.13→1.15 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3208

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LSG

3lsg


Resolution: 1.13→29.695 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.24
RfactorNum. reflection% reflection
Rfree0.1811 1810 4.95 %
Rwork0.1584 --
obs0.1595 36575 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 47.98 Å2 / Biso mean: 15.6736 Å2 / Biso min: 6.59 Å2
Refinement stepCycle: final / Resolution: 1.13→29.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 0 136 1133
Biso mean---26 -
Num. residues----121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.13-1.16010.26511050.215225984
1.1601-1.19420.2941270.2122258397
1.1942-1.23270.22231350.1852675100
1.2327-1.27680.2191370.16142683100
1.2768-1.32790.18591370.15382671100
1.3279-1.38840.17341380.14452700100
1.3884-1.46160.17641600.13612642100
1.4616-1.55310.15541530.12522696100
1.5531-1.6730.14721490.13142716100
1.673-1.84140.20891440.15052698100
1.8414-2.10780.16821540.1482718100
2.1078-2.65530.19251450.15742785100
2.6553-29.6950.16281260.17092939100

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