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- PDB-6o8n: Crystal Structure of C9S tetrasulfide state of Sulfide-responsive... -

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Basic information

Entry
Database: PDB / ID: 6o8n
TitleCrystal Structure of C9S tetrasulfide state of 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
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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...: / 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, ArsR family
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, ArsR family
B: Transcriptional regulator, ArsR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1045
Polymers24,8162
Non-polymers2883
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-66 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.837, 84.837, 57.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21A-443-

HOH

31A-447-

HOH

41B-321-

HOH

51B-393-

HOH

61B-411-

HOH

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Components

#1: Protein Transcriptional regulator, ArsR family


Mass: 12408.018 Da / Num. of mol.: 2 / Mutation: C9S
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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Ammonium sulfate 0.2M, Na Calcodyate 0.1M pH 6.5, 30% PEG 8000, Protein buffer: 20 mM Tris pH 8, 200 mM NaCl, 2mM EDTA, 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: 1.000031 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 1.95→59.99 Å / Num. obs: 15799 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rpim(I) all: 0.047 / Rrim(I) all: 0.174 / Rsym value: 0.167 / Net I/σ(I): 14.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 13 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2594 / CC1/2: 0.79 / Rpim(I) all: 0.34 / Rsym value: 1.147 / % possible all: 100

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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: 1.95→47.459 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 738 5 %
Rwork0.2083 --
obs0.2102 14749 93.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→47.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 15 313 1819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011517
X-RAY DIFFRACTIONf_angle_d0.4362038
X-RAY DIFFRACTIONf_dihedral_angle_d0.519702
X-RAY DIFFRACTIONf_chiral_restr0.031234
X-RAY DIFFRACTIONf_plane_restr0.001259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9502-2.10070.26481480.21672594X-RAY DIFFRACTION89
2.1007-2.31210.25251350.25312480X-RAY DIFFRACTION84
2.3121-2.64670.27811280.21592868X-RAY DIFFRACTION96
2.6467-3.33440.25321580.20522948X-RAY DIFFRACTION98
3.3344-47.47350.22361690.18853121X-RAY DIFFRACTION99

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