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- PDB-1en3: 1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING A... -
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Basic information
Entry | Database: PDB / ID: 1en3 | ||||||||||||||||||
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Title | 1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / DIVALENT CATIONS / DNA SEQUENCE-SPECIFIC BINDING / SHELXDNA / B-DNA | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() ![]() Chiu, T.K. / Dickerson, R.E. | ![]() ![]() Title: 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. Authors: Chiu, T.K. / Dickerson, R.E. #1: ![]() Title: Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG. Authors: Chiu, T.K. / Kaczor-Grzeskowiak, M. / Dickerson, R.E. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 31.7 KB | Display | ![]() |
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PDB format | ![]() | 21.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 385.4 KB | Display | ![]() |
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Full document | ![]() | 395.4 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1en8C ![]() 1en9C ![]() 1eneC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA chain | Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 37.9 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 275 K / Method: vapor diffusion, sitting drop Details: INITIAL CONCENTRATION IN DROPLET: 0.24 MM DNA, 8.57 MM MAGNESIUM ACETATE, 0.11 MM STREPTONIGRIN, 10-15% MPD, 45% FINAL MPD CONCENTRATION IN RESERVOIR. SOLUTIONS WERE UNBUFFERED, VAPOR ...Details: INITIAL CONCENTRATION IN DROPLET: 0.24 MM DNA, 8.57 MM MAGNESIUM ACETATE, 0.11 MM STREPTONIGRIN, 10-15% MPD, 45% FINAL MPD CONCENTRATION IN RESERVOIR. SOLUTIONS WERE UNBUFFERED, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 0.985→8 Å / Num. all: 13464 / Num. obs: 13464 / % possible obs: 95 % / Observed criterion σ(I): -1 / Redundancy: 5.75 % / Biso Wilson estimate: 5.3 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 0.985→1.016 Å / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 7.4 / % possible all: 90.7 |
Reflection | *PLUS Num. measured all: 77354 |
Reflection shell | *PLUS % possible obs: 90.7 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: BDJ019 Resolution: 0.985→8 Å / Num. parameters: 17441 / Num. restraintsaints: 2945 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL. Details: REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT ...Details: REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT LEAST-SQUARES IN SHELXL-97. THE TOP 50 MOST DISAGREEABLE REFLECTIONS WERE REJECTED TOWARDS THE LATTER STAGES OF REFINEMENT BUT THESE ARE STILL INCLUDED IN THE RELEASED DATA.
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Solvent computation | Solvent model: SWAT 0.814695 0.4550 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 14 / Occupancy sum hydrogen: 114 / Occupancy sum non hydrogen: 272.84 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.985→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.2395 / Rfactor Rwork: 0.1529 |