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Yorodumi- PDB-2gvr: Crystal structure of the berenil-D(CGCGAATTCGCG)2 complex at 1.65... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gvr | ||||||||||||||||||
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Title | Crystal structure of the berenil-D(CGCGAATTCGCG)2 complex at 1.65 A resolution. | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / NUCLEIC ACIDS / DOUBLE HELIX / MINOR GROOVE / CRYSTAL STRUCTURE OF B-DNA / DNA MINOR GROOVE BINDER / DICKERSON AND DREW DODECAMER / D(CGCGAATTCGCG)2 / A2T2 / DNA MINOR GROOVE-LIGAND COMPLEX / DNA-DRUG COMPLEX / DNA HYDRATION / BERENIL AND DNA / BERENIL-DNA COMPLEX / MAGNESIUM-WATER COMPLEX / HYDRATED MAGNESIUM COMPLEX. | Function / homology | BERENIL / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | Authors | Lee, M.P.H. / Parkinson, G.N. / Neidle, S. | Citation | Journal: To be Published | Title: Crystal structure of the berenil-D(CGCGAATTCGCG)2 complex at 1.65 A resolution. Authors: Neidle, S. / Parkinson, G.N. / Lee, M.P.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gvr.cif.gz | 25.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gvr.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 2gvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/2gvr ftp://data.pdbj.org/pub/pdb/validation_reports/gv/2gvr | HTTPS FTP |
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-Related structure data
Related structure data | 2dbeS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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: AT-RICH REGION IN THE GENOME OF ORGANISMS. #2: Chemical | ChemComp-BRN / | #3: Chemical | ChemComp-MG / | #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: 2.05 Å3/Da / Density % sol: 40.13 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / pH: 6.5 Details: MAGNESIUM CHLORIDE, DNA, BERENIL, MPD, SODIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING DROP, temperature 285K, pH 6.50 | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 4, 2002 / Details: OSMIC FOCUSING MIRROR SYSTEM |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→17 Å / Num. obs: 7822 / % possible obs: 96.5 % / Observed criterion σ(I): -2 / Redundancy: 4.95 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 58.04 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 12.65 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE. Resolution: 1.65→8 Å / Num. parameters: 2363 / Num. restraintsaints: 2511 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.59 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 587 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→8 Å
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Refine LS restraints |
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