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Open data
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Basic information
Entry | Database: PDB / ID: 2plb | ||||||||||||||||||
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Title | D(GTATACC) under hydrostatic pressure of 1.39 GPa | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / HIGH-PRESSURE | Function / homology | SPERMINE / DNA | ![]() Method | ![]() ![]() ![]() ![]() Prange, T. / Girard, E. / Kahn, R. / Fourme, R. | ![]() ![]() Title: Adaptation of the base-paired double-helix molecular architecture to extreme pressure. Authors: Girard, E. / Prange, T. / Dhaussy, A.C. / Migianu-Griffoni, E. / Lecouvey, M. / Chervin, J.C. / Mezouar, M. / Kahn, R. / Fourme, R. #1: Journal: Nature / Year: 1989 Title: Coexistence of A-and B-Form DNA in a Single Crystal Lattice Authors: Doucet, J. / Benoit, J.-P. / Cruse, W.B.T. / Prange, T. / Kennard, O. #2: Journal: J.Synchrotron Radia. / Year: 2001 Title: High-pressure protein crystallography (HPPX): Instrumentation, methodology and results on lysozyme crystals Authors: Fourme, R. / Kahn, R. / Mezouar, M. / Girard, E. / Horentrup, C. / Prange, T. / Ascone, I. #3: ![]() Title: High pressure macromolecular crystallography: The 140 MPa crystal structure at 2.3 A resolution of urate oxidase, A 135 KD tetrameric assembly Authors: Colloc'h, N. / Girard, E. / Dhaussy, A.C. / Kahn, R. / Ascone, I. / Mezouar, M. / Fourme, R. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22 KB | Display | ![]() |
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PDB format | ![]() | 13.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 392.3 KB | Display | ![]() |
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Full document | ![]() | 396.3 KB | Display | |
Data in XML | ![]() | 4.9 KB | Display | |
Data in CIF | ![]() | 6.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pkvC ![]() 2pl4C ![]() 2pl8SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA octamer #2: Chemical | ChemComp-SPM / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.84 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20 mg of DNA dissolved in 0.2 ml of 15% MPD solution cacodylate buffer 10-2 M. Additives: 10-5 M sodium azide, 10-2 M MgCl2, 2.10-2 M spermine chloride. Reservoir: same solution but 50 % ...Details: 20 mg of DNA dissolved in 0.2 ml of 15% MPD solution cacodylate buffer 10-2 M. Additives: 10-5 M sodium azide, 10-2 M MgCl2, 2.10-2 M spermine chloride. Reservoir: same solution but 50 % MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 10, 2006 / Details: 2 crystals, parallel beam, no focusing |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.3738 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→10 Å / Num. all: 5582 / Num. obs: 5518 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.1 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.2 / Num. unique all: 490 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PL8 Resolution: 1.6→10 Å / Num. parameters: 1747 / Num. restraintsaints: 1776 / Isotropic thermal model: individual restrained B factors / Cross valid method: FREE R / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER Details: One sugar and one phosphate group are disordered (two positions). The spermine molecule is also disordered
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Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 178 / Occupancy sum non hydrogen: 412 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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