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- PDB-6o8l: Crystal Structure of C9S apo and reduced Sulfide-responsive trans... -

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Basic information

Entry
Database: PDB / ID: 6o8l
TitleCrystal Structure of C9S 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
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: 1.36 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


Theoretical massNumber of molelcules
Total (without water)12,3121
Polymers12,3121
Non-polymers00
Water1,62190
1
A: Transcriptional regulator, ArsR family

A: Transcriptional regulator, ArsR family


Theoretical massNumber of molelcules
Total (without water)24,6242
Polymers24,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area2470 Å2
ΔGint-25 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.375, 46.375, 159.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-234-

HOH

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Components

#1: Protein Transcriptional regulator, ArsR family


Mass: 12311.889 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystallization condition: sodium citrate 1.8 M pH 6.4; 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: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072152 Å / Relative weight: 1
ReflectionResolution: 1.36→53.21 Å / Num. obs: 22858 / % possible obs: 97.3 % / Redundancy: 17.4 % / CC1/2: 1 / Rpim(I) all: 0.009 / Rrim(I) all: 0.0039 / Rsym value: 0.038 / Net I/σ(I): 44.3
Reflection shellResolution: 1.36→1.41 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 2 / CC1/2: 0.757 / Rrim(I) all: 0.911 / % possible all: 89.9

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Processing

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

3pqj


Resolution: 1.36→28.309 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.87
RfactorNum. reflection% reflection
Rfree0.1882 1094 4.93 %
Rwork0.148 --
obs0.15 22170 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.36→28.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms709 0 0 90 799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006736
X-RAY DIFFRACTIONf_angle_d0.88991
X-RAY DIFFRACTIONf_dihedral_angle_d2.124444
X-RAY DIFFRACTIONf_chiral_restr0.062115
X-RAY DIFFRACTIONf_plane_restr0.004128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.42190.21371000.16922161X-RAY DIFFRACTION83
1.4219-1.49690.20821420.14472569X-RAY DIFFRACTION97
1.4969-1.59060.19491410.12722635X-RAY DIFFRACTION100
1.5906-1.71340.16151160.12052693X-RAY DIFFRACTION100
1.7134-1.88580.1931630.12572650X-RAY DIFFRACTION100
1.8858-2.15860.15641440.12152716X-RAY DIFFRACTION100
2.1586-2.71930.18271510.14652769X-RAY DIFFRACTION100
2.7193-28.31540.2031370.16952883X-RAY DIFFRACTION97

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