+Open data
-Basic information
Entry | Database: PDB / ID: 2og0 | ||||||
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Title | Crystal Structure of the Lambda Xis-DNA complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / DNA ARCHITECTURAL PROTEIN / 'WINGED'HELIX PROTEIN / PHAGE EXCISION / SITE-SPECIFIC RECOMBINATION RECOMBINATION / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information provirus excision / DNA recombination / DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage lambda (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Papagiannis, C.V. / Sam, M.D. / Abbani, M.A. / Cascio, D. / Yoo, D. / Clubb, R.T. / Johnson, R.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Fis targets assembly of the xis nucleoprotein filament to promote excisive recombination by phage lambda. Authors: Papagiannis, C.V. / Sam, M.D. / Abbani, M.A. / Yoo, D. / Cascio, D. / Clubb, R.T. / 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 | 2og0.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2og0.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 2og0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/2og0 ftp://data.pdbj.org/pub/pdb/validation_reports/og/2og0 | HTTPS FTP |
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-Related structure data
Related structure data | 1rh6S 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: DNA chain | Mass: 5542.596 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 5485.622 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 6425.388 Da / Num. of mol.: 2 / Fragment: XIS (Residues: 1-55) / Mutation: C28S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Strain: VIRUS / Gene: xis / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03699 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.65 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% Polyethylene Glycol monomethyl ether 2000, 0.2 M Ammonium Sulfate and 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 29, 2004 / Details: Mirrors |
Radiation | Monochromator: Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→80 Å / Num. all: 15654 / Num. obs: 15654 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.32 % / Biso Wilson estimate: 37.5 Å2 / Rsym value: 0.071 / Χ2: 1.038 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.71 / Num. unique all: 1330 / Rsym value: 0.409 / Χ2: 0.996 / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RH6 Resolution: 1.9→54.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.058 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.168 / 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 mean: 26.393 Å2
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Refine analyze | Luzzati coordinate error free: 0.1868 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→54.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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