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- PDB-6swf: Selenomethionine derivative of the REC domain of AraT, a response... -

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Basic information

Entry
Database: PDB / ID: 6swf
TitleSelenomethionine derivative of the REC domain of AraT, a response regulator from Geobacillus stearothermophilus
ComponentsTwo-component response regulator
KeywordsTRANSCRIPTION / Response regulator / two component sensing system / Geobacillus stearothermophilus / arabinan utilization system
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / 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 ...Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / 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 / SAD / Resolution: 2.601 Å
AuthorsLansky, S. / Lavid, N. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Selenomethionine derivative of the REC domain of AraT, a response regulator from Geobacillus stearothermophilus
Authors: Lansky, S. / Lavid, N. / Shoham, Y. / Shoham, G.
History
DepositionSep 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Two-component response regulator
B: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)31,5762
Polymers31,5762
Non-polymers00
Water77543
1
A: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7881
Polymers15,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)15,7881
Polymers15,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.131, 32.892, 78.656
Angle α, β, γ (deg.)90.000, 97.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Two-component response regulator


Mass: 15788.048 Da / Num. of mol.: 2
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.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 41% PPG 425 and 0.1 M Bis-Tris pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 7778 / % possible obs: 99.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 13.3
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 765 / % possible all: 98.2

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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: SAD / Resolution: 2.601→39.01 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3253 725 9.37 %
Rwork0.2354 7016 -
obs0.2434 7741 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.55 Å2 / Biso mean: 30.0137 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 2.601→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 0 43 2151
Biso mean---29.29 -
Num. residues----258
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.601-2.80140.35281460.2687137999
2.8014-3.08320.38041370.26971380100
3.0832-3.52910.34651430.245140299
3.5291-4.44530.29481250.2152142699
4.4453-39.010.30431740.2196142999

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