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- PDB-6o8m: Crystal Structure of C9S apo Sulfide-responsive transcriptional r... -

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Basic information

Entry
Database: PDB / ID: 6o8m
TitleCrystal Structure of C9S apo Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulated bound to diamide (tetramethylazodicarboxamide).
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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-LSY / Transcriptional regulator, ArsR family
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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)12,4862
Polymers12,3121
Non-polymers1741
Water1,44180
1
A: Transcriptional regulator, ArsR family
hetero molecules

A: Transcriptional regulator, ArsR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9724
Polymers24,6242
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2850 Å2
ΔGint-25 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.509, 46.509, 158.468
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-358-

HOH

21A-376-

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: Chemical ChemComp-LSY / N~1~,N~1~,N~2~,N~2~-tetramethylhydrazine-1,2-dicarboxamide


Mass: 174.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 38.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystallization buffer : sodium citrate 1.8 M pH=6.4, 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: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 1.46→52.82 Å / Num. obs: 17998 / % possible obs: 99.9 % / Redundancy: 18.4 % / CC1/2: 1 / Rpim(I) all: 0.012 / Rrim(I) all: 0.051 / Rsym value: 0.05 / Net I/σ(I): 33.9
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2546 / CC1/2: 0.875 / Rpim(I) all: 0.273 / Rrim(I) all: 0.984 / % 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: 1.46→40.278 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.68
RfactorNum. reflection% reflection
Rfree0.1775 879 4.88 %
Rwork0.1446 --
obs0.1462 17998 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.46→40.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 0 80 832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008741
X-RAY DIFFRACTIONf_angle_d0.998994
X-RAY DIFFRACTIONf_dihedral_angle_d2.756274
X-RAY DIFFRACTIONf_chiral_restr0.064116
X-RAY DIFFRACTIONf_plane_restr0.005128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4602-1.55170.2221400.14752546X-RAY DIFFRACTION89
1.5517-1.67150.17891410.12392723X-RAY DIFFRACTION95
1.6715-1.83970.19461460.11252836X-RAY DIFFRACTION98
1.8397-2.10590.12521400.10782892X-RAY DIFFRACTION99
2.1059-2.65320.14761400.1382972X-RAY DIFFRACTION100
2.6532-40.29330.19921720.16453150X-RAY DIFFRACTION99

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