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- PDB-3s5r: Crystal structure of a putative transcriptional regulator of the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3s5r | ||||||
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Title | Crystal structure of a putative transcriptional regulator of the TETR family (SYN_02108) from Syntrophus aciditrophicus at 2.60 A resolution | ||||||
![]() | Transcriptional regulator TetR family | ||||||
![]() | DNA BINDING PROTEIN / DNA/RNA-binding 3-helical bundle / Tetracyclin repressor-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of a Putative transcriptional regulator of the TetR family (SYN_02108) from Syntrophus aciditrophicus SB at 2.60 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.5 KB | Display | ![]() |
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PDB format | ![]() | 132.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.1 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Details | CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
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Components
#1: Protein | Mass: 24427.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15.00% Glycerol, 8.500% iso-Propanol, 17.00% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 9, 2011 / Details: double crystal monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→29.279 Å / Num. obs: 16314 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.791 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. PEG-4000 FRAGMENTS(PEG) FROM THE CRYSTALLIZATION CONDITION AND 1,2 ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE REFINEMENT WAS RESTRAINED WITH THE MAD PHASES.
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Displacement parameters | Biso max: 186.07 Å2 / Biso mean: 82.9865 Å2 / Biso min: 49.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→29.279 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.78 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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