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- PDB-3gf2: Crystal structure of the hypothetical regulator ST1710 complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gf2 | ||||||
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Title | Crystal structure of the hypothetical regulator ST1710 complexed with sodium salicylate | ||||||
![]() | 146aa long hypothetical transcriptional regulator | ||||||
![]() | TRANSCRIPTION / Transcription regulator / ST1710 / MarR / DNA-binding / Transcription regulation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() response to stress / DNA-binding transcription factor activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Kumarevel, T. / Tanaka, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators. Authors: Kumarevel, T. / Tanaka, T. / Umehara, T. / Yokoyama, S. #1: ![]() Title: Crystal structure of the MarR family regulatory protein, ST1710, from Sulfolobus tokodaii strain 7. Authors: Kumarevel, T. / Tanaka, T. / Nishio, M. / Gopinath, S.C. / Takio, K. / Shinkai, A. / Kumar, P.K. / Yokoyama, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.8 KB | Display | ![]() |
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PDB format | ![]() | 31.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3gezC ![]() 3gfiC ![]() 3gfjC ![]() 3gflC ![]() 3gfmC ![]() 2eb7S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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: 16879.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SAL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18% PEG 8000, 0.2M Calcium acetate, 0.1M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 13381 / Num. obs: 13381 / % possible obs: 91.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.6 % / Num. unique all: 1425 / Rsym value: 0.264 / % possible all: 99.8 |
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Processing
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Refinement | Starting model: 2EB7 Resolution: 1.8→19.76 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 271895 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.181 Å2 / ksol: 0.374 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.17 Å2 / Biso mean: 29.642 Å2 / Biso min: 10.78 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
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Xplor file |
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