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Yorodumi- PDB-3jra: Crystal structure of Fis bound to 27bp non consensus sequence DNA F6 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jra | ||||||
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Title | Crystal structure of Fis bound to 27bp non consensus sequence DNA F6 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Protein-DNA complex / HTH domain / 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 / 3IV5 / Resolution: 3.11 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 | 3jra.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jra.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jra_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 3jra_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 3jra_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 3jra_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/3jra ftp://data.pdbj.org/pub/pdb/validation_reports/jr/3jra | HTTPS FTP |
-Related structure data
Related structure data | 3iv5C 3jr9C 3jrbC 3jrcC 3jrdC 3jreC 3jrfC 3jrgC 3jrhC 3jriC C: citing same article (ref.) |
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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: 8254.367 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: DNA chain | | Mass: 8330.447 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: 4.08 Å3/Da / Density % sol: 69.84 % |
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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: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3.1→90 Å / Num. obs: 11963 / % possible obs: 97.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.139 / Χ2: 1.825 / Net I/σ(I): 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: 3IV5 / Resolution: 3.11→81.11 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.384 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 9.911 / ESU R Free: 0.453 / 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: 56.28 Å2 / Biso mean: 48.163 Å2 / Biso min: 15.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.11→81.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.11→3.191 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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