+Open data
-Basic information
Entry | Database: PDB / ID: 1jes | ||||||||||||||||||
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Title | Crystal Structure of a Copper-Mediated Base Pair in DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Cu / copper / Z-DNA / dodecamer / duplex / unnatural / designed | Function / homology | COPPER (II) ION / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | Authors | Atwell, S. / Meggers, E. / Spraggon, G. / Schultz, P.G. | Citation | Journal: J.Am.Chem.Soc. / Year: 2001 Title: Structure of a Copper-Mediated Base Pair in DNA Authors: Atwell, S. / Meggers, E. / Spraggon, G. / Schultz, P.G. #1: Journal: J.Am.Chem.Soc. / Year: 2000 Title: A Novel Copper-Mediated DNA Base Pair Authors: Meggers, E. / Holland, P.L. / Tolman, W.B. / Romesberg, F.E. / Schultz, P.G. #2: Journal: Science / Year: 1981 Title: Left-handed double helical DNA: variations in the backbone conformation Authors: Wang, A.G.-J. / Quigley, G.J. / Kolpak, F.J. / van Der Marel, G. / van Boom, J.H. / Rich, A. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981 Title: Structure of a B-DNA dodecamer: conformation and dynamics Authors: Drew, H.R. / Wing, R.M. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jes.cif.gz | 25.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jes.ent.gz | 17.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/1jes ftp://data.pdbj.org/pub/pdb/validation_reports/je/1jes | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 3648.371 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #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: 1.82 Å3/Da / Density % sol: 32.43 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% MPD, 40 mM Na Cacodylate, 12 mM Spermine tetra-HCl, 80 mM NaCl, 20 mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 140 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.37991,1.37791,1.0 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2001 / Details: Curved Si (111) | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→50 Å / Num. all: 47272 / Num. obs: 47190 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 14.058 Å2 / Rsym value: 0.096 / Net I/σ(I): 46.7 | ||||||||||||
Reflection shell | Resolution: 1.49→1.54 Å / Rmerge(I) obs: 0.686 / % possible all: 84.1 | ||||||||||||
Reflection | *PLUS Num. obs: 8531 / Num. measured all: 47272 / Rmerge(I) obs: 0.096 | ||||||||||||
Reflection shell | *PLUS % possible obs: 84.1 % / Rmerge(I) obs: 0.686 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: initial map fit with mononucleotides Resolution: 1.5→50 Å / Cross valid method: free r / σ(F): 0 / σ(I): 0 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: The fofc maps indicated an alternate conformation for the phosphate of B23, and so the structure was refined with two conformations for the phosphate of B23 (excepting the O5') and most of ...Details: The fofc maps indicated an alternate conformation for the phosphate of B23, and so the structure was refined with two conformations for the phosphate of B23 (excepting the O5') and most of residue B22 (excepting O5'), each with 0.5 occupancy.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. reflection obs: 8531 / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.169 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |