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- PDB-6o8o: Crystal Structure of C9S disulfide state of Sulfide-responsive tr... -

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Basic information

Entry
Database: PDB / ID: 6o8o
TitleCrystal Structure of C9S disulfide state of Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulatus.
ComponentsTranscriptional regulator, ArsR familyTranscriptional regulation
KeywordsTRANSCRIPTION / transcription factor / sulfide sensor / reactive sulfur species / photosynthesis regulation
Function / homologyBacterial 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 / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / Transcriptional regulator, ArsR family
Function and homology information
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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

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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
C: Transcriptional regulator, ArsR family
D: Transcriptional regulator, ArsR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,02916
Polymers49,9984
Non-polymers1,03212
Water1,04558
1
A: Transcriptional regulator, ArsR family
B: Transcriptional regulator, ArsR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4197
Polymers24,9992
Non-polymers4205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-78 kcal/mol
Surface area11680 Å2
MethodPISA
2
C: Transcriptional regulator, ArsR family
D: Transcriptional regulator, ArsR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6119
Polymers24,9992
Non-polymers6127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-85 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 92.600, 148.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Transcriptional regulator, ArsR family / Transcriptional regulation


Mass: 12499.469 Da / Num. of mol.: 4 / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystallization buffer: 0.1M Bis-tris propane pH 5.5-6.5, 1.6-1.85M Ammonium sulfate; 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: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→49.66 Å / Num. obs: 24511 / % possible obs: 99.7 % / Redundancy: 21.1 % / CC1/2: 1 / Rpim(I) all: 0.025 / Rrim(I) all: 0.115 / Rsym value: 0.112 / Net I/σ(I): 27.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 18.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2489 / CC1/2: 0.66 / Rpim(I) all: 0.622 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→49.66 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1178 4.81 %
Rwork0.2291 --
obs0.2307 24511 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 52 58 3217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033197
X-RAY DIFFRACTIONf_angle_d0.5254305
X-RAY DIFFRACTIONf_dihedral_angle_d4.5882162
X-RAY DIFFRACTIONf_chiral_restr0.036491
X-RAY DIFFRACTIONf_plane_restr0.002550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61380.41621200.31062489X-RAY DIFFRACTION82
2.6138-2.75160.2851400.28632686X-RAY DIFFRACTION88
2.7516-2.9240.3231330.26522874X-RAY DIFFRACTION93
2.924-3.14970.31971190.26382967X-RAY DIFFRACTION96
3.1497-3.46660.281770.25773004X-RAY DIFFRACTION98
3.4666-3.9680.28111530.23362897X-RAY DIFFRACTION93
3.968-4.99850.21941680.18983133X-RAY DIFFRACTION99
4.9985-49.66980.23281680.21193283X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.5239 Å / Origin y: -28.3998 Å / Origin z: -2.3144 Å
111213212223313233
T0.4393 Å2-0.2123 Å20.0671 Å2-0.2964 Å2-0.0389 Å2--0.3333 Å2
L0.1521 °2-0.0255 °20.1871 °2-0.3285 °20.3373 °2--0.6335 °2
S-0.0504 Å °0.0724 Å °0.0184 Å °0.1853 Å °-0.0282 Å °0.0772 Å °-0.0891 Å °-0.0757 Å °-0.0016 Å °
Refinement TLS groupSelection details: all

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