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- PDB-3gez: Crystal Structure of the hypothetical egulator from Sulfolobus to... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gez | ||||||
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Title | Crystal Structure of the hypothetical egulator from Sulfolobus tokodaii 7 | ||||||
![]() | 146aa long hypothetical transcriptional regulator | ||||||
![]() | 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 | ![]() | 45.7 KB | Display | ![]() |
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PDB format | ![]() | 31 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.5 KB | Display | ![]() |
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Full document | ![]() | 423.7 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gf2C ![]() 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-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.41 % |
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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 10, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 10380 / Num. obs: 10380 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 18.5 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.104 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 19.1 % / Num. unique all: 973 / Rsym value: 0.321 / % possible all: 94.4 |
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Processing
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Refinement | Starting model: 2EB7 Resolution: 2→19.74 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 115851 / 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: 48.069 Å2 / ksol: 0.338 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.85 Å2 / Biso mean: 31.812 Å2 / Biso min: 6.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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