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Yorodumi- PDB-3jr9: Crystal structure of Fis bound to 27 bp optimal binding sequence F2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jr9 | ||||||
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Title | Crystal structure of Fis bound to 27 bp optimal binding sequence F2 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / HTH domain / Protein-DNA complex / minor groove compression / DNA bending / indirect recognition / activator / DNA-binding / Transcription / Transcription regulation / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / protein-DNA complex ...invertasome / positive regulation of DNA recombination / sequence-specific DNA binding, bending / provirus excision / nucleoid / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / chromosome organization / core promoter sequence-specific DNA binding / protein-DNA complex / response to radiation / nucleosome / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Stella, S. / Cascio, D. / Johnson, R.C. | ||||||
Citation | Journal: Genes Dev. / Year: 2010 Title: The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. Authors: Stella, S. / Cascio, D. / Johnson, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jr9.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jr9.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jr9_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 3jr9_full_validation.pdf.gz | 457.6 KB | Display | |
Data in XML | 3jr9_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 3jr9_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/3jr9 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/3jr9 | HTTPS FTP |
-Related structure data
Related structure data | 3iv5C 3jraC 3jrbC 3jrcC 3jrdC 3jreC 3jrfC 3jrgC 3jrhC 3jriC 1etoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11252.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: fis, b3261, JW3229 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6R3 #2: DNA chain | | Mass: 8318.416 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: DNA chain | | Mass: 8265.410 Da / Num. of mol.: 1 / Source method: obtained synthetically #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Sodium citrate, 0.1 M TRIS-HCl pH 8.5, 36% PEG 400, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→90 Å / Num. obs: 14353 / % possible obs: 99 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.165 / Χ2: 1.475 / Net I/σ(I): 6.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ETO Resolution: 2.9→39.41 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.929 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.12 Å2 / Biso mean: 40.851 Å2 / Biso min: 5.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→39.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.903→2.978 Å / Total num. of bins used: 20
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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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