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- PDB-6o8k: Crystal Structure of apo and reduced Sulfide-responsive transcrip... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6o8k | ||||||
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Title | Crystal Structure of apo and reduced Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulatus. | ||||||
![]() | Transcriptional regulator, ArsR family | ||||||
![]() | TRANSCRIPTION / transcription factor / sulfide sensor / reactive sulfur species / photosynthesis regulation | ||||||
Function / homology | 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 / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / Transcriptional regulator, ArsR family![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Capdevila, D.A. / Gonzalez-Gutierrez, G. / Giedroc, D.P. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54 KB | Display | ![]() |
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PDB format | ![]() | 37.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 271.1 KB | Display | ![]() |
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Full document | ![]() | 271.1 KB | Display | |
Data in XML | ![]() | 1.2 KB | Display | |
Data in CIF | ![]() | 2.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6o8lC ![]() 6o8mC ![]() 6o8nC ![]() 6o8oC ![]() 3pqkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12327.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.38 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jun 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072152 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.12→2.19 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→28.778 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 21.363 Å / Origin y: -19.1309 Å / Origin z: -3.0157 Å
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Refinement TLS group | Selection details: all |