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- PDB-1xhe: Crystal structure of the receiver domain of redox response regula... -

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Basic information

Entry
Database: PDB / ID: 1xhe
TitleCrystal structure of the receiver domain of redox response regulator arca
ComponentsAerobic respiration control protein arcA
KeywordsTRANSCRIPTION / Two-Component System / Gene Regulation / Transcription Factor / Anoxic Redox Control / Doubly Wound Five-Stranded Beta/Alpha Fold
Function / homology
Function and homology information


phosphorelay response regulator activity / DNA-binding transcription repressor activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / 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. ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / 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 / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aerobic respiration control protein ArcA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsToro-Roman, A. / Mack, T.R. / Stock, A.M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural Analysis and Solution Studies of the Activated Regulatory Domain of the Response Regulator ArcA: A Symmetric Dimer Mediated by the alpha4-beta5-alpha5 Face
Authors: Toro-Roman, A. / Mack, T.R. / Stock, A.M.
History
DepositionSep 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aerobic respiration control protein arcA
B: Aerobic respiration control protein arcA


Theoretical massNumber of molelcules
Total (without water)28,0062
Polymers28,0062
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.695, 86.695, 214.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-157-

HOH

DetailsBiological assembly is a homodimer present in the assymetric unit.

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Components

#1: Protein Aerobic respiration control protein arcA / Redox Response Regulator ArcA / Dye resistance protein


Mass: 14002.975 Da / Num. of mol.: 2 / Fragment: Receiver Domain / Mutation: N123Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: arcA, dye, fexA, sfrA, seg, msp, cpxC / Plasmid: pEF29 (pJES307 derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS and BL21(DE3) / References: UniProt: P0A9Q1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium Acetate, MPD, Sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.97896
SYNCHROTRONNSLS X4A20.97139
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 25, 2003
ADSC QUANTUM 42CCDSep 25, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1KOHZU Double Crystal Monochromator With A Sagittally Focused Second Crystal. Crystal Type Is Si(111)SINGLE WAVELENGTHMx-ray1
2KOHZU Double Crystal Monochromator With A Sagittally Focused Second Crystal. Crystal Type Is Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.971391
ReflectionResolution: 2.5→74.536 Å / Num. all: 17401 / Num. obs: 17085 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.7 Å2 / Limit h max: 30 / Limit h min: 0 / Limit k max: 17 / Limit k min: 0 / Limit l max: 86 / Limit l min: 0 / Net I/σ(I): 18.2
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 2.9 / Num. unique all: 1604 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: SAD
Starting model: Peak-Wavelength Derived Phases

Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / SU B: 6.545 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.23
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.25647 864 5.1 %RANDOM
Rwork0.21269 ---
all0.21488 17076 --
obs0.21488 17076 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.617 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.71 Å20 Å2
2--1.41 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 0 69 1990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221945
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.982633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055241
X-RAY DIFFRACTIONr_chiral_restr0.1010.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021451
X-RAY DIFFRACTIONr_nbd_refined0.2480.3908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.5193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.516
X-RAY DIFFRACTIONr_mcbond_it1.76321207
X-RAY DIFFRACTIONr_mcangle_it3.13731951
X-RAY DIFFRACTIONr_scbond_it1.6472738
X-RAY DIFFRACTIONr_scangle_it2.683682
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.33 57
Rwork0.256 1133
obs-1133

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