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- PDB-6o8n: Crystal Structure of C9S tetrasulfide state of Sulfide-responsive... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6o8n | ||||||
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Title | Crystal Structure of C9S tetrasulfide state of Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulatus. | ||||||
![]() | Transcriptional regulator, ArsR family | ||||||
![]() | TRANSCRIPTION / transcription factor / sulfide sensor / reactive sulfur species / photosynthesis regulation | ||||||
Function / homology | ![]() | ||||||
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 | ![]() | 61.3 KB | Display | ![]() |
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PDB format | ![]() | 42.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.7 KB | Display | ![]() |
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Full document | ![]() | 449.8 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6o8kC ![]() 6o8lC ![]() 6o8mC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12408.018 Da / Num. of mol.: 2 / Mutation: C9S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 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 |
-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: Sep 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000031 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→47.459 Å
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Refine LS restraints |
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LS refinement shell |
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