+Open data
-Basic information
Entry | Database: PDB / ID: 7zqm | ||||||||||||||||||||||||||||
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Title | d(CGCGCG)2 Z-DNA AT 3000 BARS (300 MPa) | ||||||||||||||||||||||||||||
Components | Z-DNA (5'-D(*Keywords | DNA / HIGH PRESSURE / DIAMOND ANVIL CELL | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.41 Å | Authors | Prange, T. / Colloc'h, N. / Girard, E. | 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 | 7zqm.cif.gz | 18.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zqm.ent.gz | 10.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zqm_validation.pdf.gz | 374.7 KB | Display | wwPDB validaton report |
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Full document | 7zqm_full_validation.pdf.gz | 374.7 KB | Display | |
Data in XML | 7zqm_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 7zqm_validation.cif.gz | 4.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/7zqm ftp://data.pdbj.org/pub/pdb/validation_reports/zq/7zqm | HTTPS FTP |
-Related structure data
Related structure data | 7zqlC 7zqnC 7zqoC 2elgS 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: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Z-DNA Hexamer under 3000 Bars hydrostatic pressure / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.7 Å3/Da / Density % sol: 27.64 % / Description: COLORLESS PRISMS |
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Crystal grow | Temperature: 298 K / Method: batch mode / pH: 6.9 Details: 10 mg in 20-30% MPD solution, cacodylatee buffer + 0.01M MGCl2 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.75003 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75003 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→25.5 Å / Num. obs: 4712 / % possible obs: 91.18 % / Redundancy: 5.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.071 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.41→1.44 Å / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 291 / CC1/2: 0.89 / Rpim(I) all: 0.177 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2ELG Resolution: 1.41→25.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.614 / SU B: 1.327 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.136 / 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: 53.78 Å2 / Biso mean: 9.859 Å2 / Biso min: 4.71 Å2
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Refinement step | Cycle: final / Resolution: 1.41→25.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.41→1.442 Å / Rfactor Rfree error: 0
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