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Yorodumi- PDB-3rh2: Crystal structure of a TetR-like transcriptional regulator (Sama_... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rh2 | ||||||
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Title | Crystal structure of a TetR-like transcriptional regulator (Sama_0099) from Shewanella amazonensis SB2B at 2.42 A resolution | ||||||
Components | Hypothetical TetR-like transcriptional regulator | ||||||
Keywords | DNA BINDING PROTEIN / DNA/RNA-binding 3-helical bundle / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-Biology | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella amazonensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.42 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Hypothetical TetR-like transcriptional regulator (Sama_0099) from SHEWANELLA AMAZONENSIS SB2B at 2.42 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rh2.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rh2.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 3rh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rh2_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 3rh2_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 3rh2_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3rh2_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/3rh2 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/3rh2 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 25121.748 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella amazonensis (bacteria) / Strain: SB2B / Gene: Sama_0099 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S1Q5 | ||||||
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#2: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically | ||||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.31 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2 | Details: 0.4M KH2PO4, 1.6M NaH2PO4, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97934,0.97915 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.42→29.118 Å / Num. obs: 15161 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 70.116 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 7.82 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.025 / Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.42→29.118 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 14.68 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.221 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.PHOSPHATE (PO4) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6.AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE LIGAND-BINDING SITE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.46 Å2 / Biso mean: 65.5524 Å2 / Biso min: 28.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→29.118 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.482 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 41.5402 Å / Origin y: 29.9371 Å / Origin z: 13.8352 Å
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