+Open data
-Basic information
Entry | Database: PDB / ID: 2pl4 | ||||||
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Title | D-(GGTATACC) under 0.55 GPa hydrostatic pressure | ||||||
Components | Synthetic DNA octamer | ||||||
Keywords | DNA / A DNA / HIGH-PRESSURE / CRYSTAL STUCTURE | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å | ||||||
Authors | Prange, T. / Girard, E. / Kahn, R. / Fourme, R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 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: Journal: BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS / Year: 2006 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. #4: Journal: J.Mol.Biol. / Year: 1987 Title: Crystal structure of hen egg-white lysozyme at a hydrostatic pressure of 1000 atmospheres. Authors: Kundrot, C.E. / Richards, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pl4.cif.gz | 20.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pl4.ent.gz | 12.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pl4_validation.pdf.gz | 369.1 KB | Display | wwPDB validaton report |
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Full document | 2pl4_full_validation.pdf.gz | 370.4 KB | Display | |
Data in XML | 2pl4_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 2pl4_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/2pl4 ftp://data.pdbj.org/pub/pdb/validation_reports/pl/2pl4 | HTTPS FTP |
-Related structure data
Related structure data | 2pkvSC 2pl8C 2plbC S: Starting model for refinement C: citing same article (ref.) |
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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: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHETIC DNA #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.72 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10 mg of octamer dissolved in cacodylate buffer (10-2 M, 15 % MPD) additives : 10-5 M sodium azide, 10-2 M MgCl2, 2.10-2 M spermine chloride. Reservoir: same solution but 50 % MPD, pH 7, ...Details: 10 mg of octamer dissolved in cacodylate buffer (10-2 M, 15 % MPD) 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: SYNCHROTRON / Site: ESRF / Beamline: ID27 / Wavelength: 0.3738 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 10, 2006 / Details: Si(111) |
Radiation | Monochromator: 2 crystals - parallel beam - no focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.3738 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→18 Å / Num. all: 5057 / Num. obs: 5057 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3.6 / Num. unique all: 741 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2PKV Resolution: 1.65→10 Å / Num. parameters: 1595 / Num. restraintsaints: 1594 / Isotropic thermal model: individual restrained B values / Cross valid method: FREE R / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 184 / Occupancy sum non hydrogen: 397 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→10 Å
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Refine LS restraints |
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