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- PDB-6o8k: Crystal Structure of apo and reduced Sulfide-responsive transcrip... -

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Basic information

Entry
Database: PDB / ID: 6o8k
TitleCrystal Structure of apo and reduced Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulatus.
ComponentsTranscriptional regulator, ArsR family
KeywordsTRANSCRIPTION / transcription factor / sulfide sensor / reactive sulfur species / photosynthesis regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
: / Bacterial regulatory protein, arsR family / 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
Transcriptional regulator, ArsR family
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsCapdevila, D.A. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118157 United States
Citation
Journal: Nat.Chem.Biol. / Year: 2021
Title: Structural basis for persulfide-sensing specificity in a transcriptional regulator.
Authors: Capdevila, D.A. / Walsh, B.J.C. / Zhang, Y. / Dietrich, C. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
#1: Journal: Biorxiv / Year: 2020
Title: Structural determinants of persulfide-sensing specificity in a dithiol-based transcriptional regulator
Authors: Capdevila, D.A. / Walsh, B.J.C. / Zhang, Y. / Dietrich, C.M. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
History
DepositionMar 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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: Transcriptional regulator, ArsR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7085
Polymers12,3281
Non-polymers3804
Water19811
1
A: Transcriptional regulator, ArsR family
hetero molecules

A: Transcriptional regulator, ArsR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,41610
Polymers24,6562
Non-polymers7618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area4080 Å2
ΔGint-99 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.849, 46.849, 163.306
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Transcriptional regulator, ArsR family


Mass: 12327.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D5AT91
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystallization buffer: 2.5M ammonium sulfate, 0.1M sodium acetate pH 4.6; Protein buffer: 20 mM Tris pH 8, 200 mM NaCl, 2mM TCEP, 2mM EDTA, 5% glycerol; SqrR 6 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072152 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072152 Å / Relative weight: 1
ReflectionResolution: 2.12→54.44 Å / Num. obs: 6628 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 1 / Rpim(I) all: 0.019 / Rrim(I) all: 0.083 / Rsym value: 0.081 / Net I/σ(I): 26.6
Reflection shellResolution: 2.12→2.19 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PQK

3pqk


Resolution: 2.12→28.778 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.27
RfactorNum. reflection% reflection
Rfree0.2642 310 4.68 %
Rwork0.2233 --
obs0.2253 6618 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→28.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms728 0 21 11 760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014751
X-RAY DIFFRACTIONf_angle_d1.291008
X-RAY DIFFRACTIONf_dihedral_angle_d9.402464
X-RAY DIFFRACTIONf_chiral_restr0.054115
X-RAY DIFFRACTIONf_plane_restr0.009126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1202-2.67090.29771460.23833041X-RAY DIFFRACTION100
2.6709-28.78110.25581640.21933267X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.363 Å / Origin y: -19.1309 Å / Origin z: -3.0157 Å
111213212223313233
T0.2238 Å20.0088 Å20.0384 Å2-0.3946 Å20.0357 Å2--0.2864 Å2
L3.101 °2-0.5758 °2-0.4317 °2-1.2785 °2-1.2305 °2--0.5674 °2
S-0.0316 Å °-0.4335 Å °0.0843 Å °-0.0403 Å °0.1493 Å °0.1736 Å °0.0401 Å °-0.1391 Å °-0.0054 Å °
Refinement TLS groupSelection details: all

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