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- PDB-6swb: The REC domain of AraT, a response regulator from Geobacillus ste... -

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Basic information

Entry
Database: PDB / ID: 6swb
TitleThe REC domain of AraT, a response regulator from Geobacillus stearothermophilus
ComponentsTwo-component response regulator
KeywordsTRANSCRIPTION / response regulator / geobacillus stearothermophilus / two component system / 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
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
DI(HYDROXYETHYL)ETHER / Two-component response regulator
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.259 Å
AuthorsLansky, S. / Lavid, N. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: 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
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
B: Two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1735
Polymers31,8542
Non-polymers3183
Water1,47782
1
A: Two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1393
Polymers15,9271
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0332
Polymers15,9271
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.499, 41.918, 43.981
Angle α, β, γ (deg.)83.460, 89.980, 71.110
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Two-component response regulator


Mass: 15927.141 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.85 Å3/Da / Density % sol: 33.6 %
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: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.259→50 Å / Num. obs: 9678 / % possible obs: 94.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.3
Reflection shellResolution: 2.259→2.4 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1203

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SWF

6swf


Resolution: 2.259→31.162 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 29.01
RfactorNum. reflection% reflection
Rfree0.2554 946 9.78 %
Rwork0.1676 --
obs0.1762 9670 94.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.94 Å2 / Biso mean: 37.108 Å2 / Biso min: 15.36 Å2
Refinement stepCycle: final / Resolution: 2.259→31.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 21 82 2232
Biso mean--50.29 41.78 -
Num. residues----259
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.259-2.37780.27411020.192993170
2.3778-2.52670.29451440.1953129298
2.5267-2.72170.30661390.1912128798
2.7217-2.99540.30821410.1896130599
2.9954-3.42830.25571490.1658128999
3.4283-4.31750.20811310.139130999
4.3175-31.1620.24211400.1645131199

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