+Open data
-Basic information
Entry | Database: PDB / ID: 7zql | ||||||||||||||||||||||||||||
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Title | d(CGCGTTAACGCG)2 B-DODECAMER AT 3100 BARS (310 MPa) | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / HIGH PRESSURE | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 Å | Authors | Prange, T. | Funding support | 1items |
Citation | Journal: Crystals / Year: 2022 Title: Behavior of B- and Z-DNA Crystals under High Hydrostatic Pressure Authors: Prange, T. / Colloc'h, N. / Dhaussy, A.C. / Lecouvey, M. / Migianu-Griffoni, E. / Girard, E. #1: 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. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zql.cif.gz | 24.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zql.ent.gz | 14.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/7zql ftp://data.pdbj.org/pub/pdb/validation_reports/zq/7zql | HTTPS FTP |
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-Related structure data
Related structure data | 7zqmC 7zqnC 7zqoC 1bnaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Dickerson's Dodecamer under hydrostatic pressure / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.28 Å3/Da / Density % sol: 46.11 % / Description: ELONGATED COLORLESS NEEDLES |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 6.9 Details: 10 micro-L of the nucleotide solution (10 mg/mL in cacodylate buffer) + 10 micro-L of a solution (20-30 % MPD + 0.01 M MGCl2) |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID27 / Wavelength: 0.3738 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2009 / Details: MONOCHROMATOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.3738 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→34 Å / Num. obs: 2412 / % possible obs: 78 % / Redundancy: 4.1 % / Biso Wilson estimate: 32 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.054 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.55→2.616 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 115 / CC1/2: 0.09 / Rpim(I) all: 0.233 / % possible all: 80.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1BNA Resolution: 2.55→17.92 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.261 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.68 Å2 / Biso mean: 22.161 Å2 / Biso min: 10.61 Å2
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Refinement step | Cycle: final / Resolution: 2.55→17.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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