+Open data
-Basic information
Entry | Database: PDB / ID: 3oie | ||||||||||||||||||
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Title | Crystal structure of the DB1880-D(CGCGAATTCGCG)2 complex | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / NUCLEIC ACIDS / DOUBLE HELIX / MINOR GROOVE / DNA MINOR GROOVE BINDER / DNA MINOR GROOVE-LIGAND COMPLEX / DB1880 / A2T2 / DICKERSON AND DREW DODECAMER / CRYSTAL STRUCTURE OF B-DNA / DNA-DRUG COMPLEX / MAGNESIUM-WATER COMPLEX / HYDRATED MAGNESIUM / DNA HYDRATION | Function / homology | Chem-881 / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | Authors | Lin, S. / Neidle, S. / Campbell, N. | Citation | Journal: To be Published | Title: Crystal structure of the DB1880-D(CGCGAATTCGCG)2 complex Authors: Lin, S. / Neidle, S. / Campbell, N. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oie.cif.gz | 29.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oie.ent.gz | 19.2 KB | Display | PDB format |
PDBx/mmJSON format | 3oie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oie_validation.pdf.gz | 657.9 KB | Display | wwPDB validaton report |
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Full document | 3oie_full_validation.pdf.gz | 664.4 KB | Display | |
Data in XML | 3oie_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 3oie_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/3oie ftp://data.pdbj.org/pub/pdb/validation_reports/oi/3oie | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: A2T2 Duplex #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-881 / | #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: 2.09 Å3/Da / Density % sol: 41.22 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MAGNESIUM CHLORIDE, DNA, COMPOUND, DB1880, MPD, SODIUM CACODYLATE BUFFER, pH 6.5, vapor diffusion, hanging drop, temperature 283K |
-Data collection
Diffraction | Mean temperature: 105 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: CCD / Detector: CCD / Date: Mar 16, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | 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→33.228 Å / Num. all: 5003 / Num. obs: 5003 / % possible obs: 96.2 % / Redundancy: 3.4 % / Rsym value: 0.036 / Net I/σ(I): 20.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→22.66 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.233 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
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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: 55.95 Å2 / Biso mean: 21.783 Å2 / Biso min: 8.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→22.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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