+Open data
-Basic information
Entry | Database: PDB / ID: 1g3v | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / nickel binding / B-DNA | Function / homology | NICKEL (II) ION / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å | Authors | Subirana, J.A. / Abrescia, N.G.A. | Citation | Journal: J.Biol.Inorg.Chem. / Year: 2002 | Title: Nickel-guanine interactions in DNA: crystal structure of nickel-d[CGTGTACACG]2. Authors: Abrescia, N.A. / Huynh-Dinh, T. / Subirana, J.A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g3v.cif.gz | 30.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g3v.ent.gz | 20 KB | Display | PDB format |
PDBx/mmJSON format | 1g3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/1g3v ftp://data.pdbj.org/pub/pdb/validation_reports/g3/1g3v | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3045.004 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Chemical | ChemComp-NI / #3: 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: 2.71 Å3/Da / Density % sol: 54.59 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: DNA, NiCl2, MPD, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9058 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9058 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. all: 2843 / Num. obs: 2843 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 15.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 3.1→3.18 Å / Rmerge(I) obs: 0.49 / Num. unique all: 213 / % possible all: 99.5 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 79.3 % / Num. measured all: 43286 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 50.2 % |
-Processing
Software |
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Refinement | Resolution: 3.1→8 Å / σ(F): 1 Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996). Details: maximum likelihood target function
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Refinement step | Cycle: LAST / Resolution: 3.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 8 Å / σ(F): 1 / Rfactor all: 0.252 / Rfactor obs: 0.209 / Rfactor Rfree: 0.271 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.1 |