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- PDB-7txm: Oxidized Structure of RexT -

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Basic information

Entry
Database: PDB / ID: 7txm
TitleOxidized Structure of RexT
ComponentsTranscriptional regulator
KeywordsDNA BINDING PROTEIN / redox sensing transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Helix-turn-helix domain / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HYDROGEN PEROXIDE / Transcriptional regulator
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsBridwell-Rabb, J. / Li, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0021240 United States
CitationJournal: Commun Biol / Year: 2022
Title: Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT.
Authors: Li, B. / Jo, M. / Liu, J. / Tian, J. / Canfield, R. / Bridwell-Rabb, J.
History
DepositionFeb 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6363
Polymers25,6022
Non-polymers341
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The biological unit is a dimer as evidenced by gel filtration chromatography and buried surface area.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-14 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.460, 100.460, 36.048
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

#1: Protein Transcriptional regulator / RexT


Mass: 12800.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr1867 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YVV6
#2: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mM MES, pH 6.3, 0.2 M ammonium chloride, 20% v/v PEG3350, 24-32% v/v glycerol, hydrogen peroxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.16→32.88 Å / Num. obs: 11404 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 41.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 19.44
Reflection shellResolution: 2.16→2.22 Å / Rmerge(I) obs: 1.431 / Num. unique obs: 1145 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
XDS1.19.2_4158data scaling
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7TXO

7txo


Resolution: 2.16→32.88 Å / SU ML: 0.3116 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.8718
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2558 1143 10.02 %
Rwork0.2002 10259 -
obs0.2058 11402 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.97 Å2
Refinement stepCycle: LAST / Resolution: 2.16→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 2 103 1716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851661
X-RAY DIFFRACTIONf_angle_d1.15092241
X-RAY DIFFRACTIONf_chiral_restr0.0616254
X-RAY DIFFRACTIONf_plane_restr0.0108292
X-RAY DIFFRACTIONf_dihedral_angle_d14.915639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.260.36931410.26771273X-RAY DIFFRACTION99.93
2.26-2.380.30881430.24161278X-RAY DIFFRACTION100
2.38-2.530.32171430.241251X-RAY DIFFRACTION100
2.53-2.720.28291420.22341276X-RAY DIFFRACTION99.93
2.72-30.27021410.23151279X-RAY DIFFRACTION100
3-3.430.25961460.20141269X-RAY DIFFRACTION99.93
3.43-4.320.23111420.17271288X-RAY DIFFRACTION99.93
4.32-32.880.22761450.18421345X-RAY DIFFRACTION99.73

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