+Open data
-Basic information
Entry | Database: PDB / ID: 7d5d | ||||||
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Title | Left-handed G-quadruplex containing one bulge | ||||||
Components | 1xBulge-LHG4motif | ||||||
Keywords | DNA / Left-handed / G-quadruplex / Bulge / Z-G4 | ||||||
Function / homology | : / SPERMINE / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | ||||||
Authors | Das, P. / Ngo, K.H. / Winnerdy, F.R. / Maity, A. / Bakalar, B. / Mechulam, Y. / Schmitt, E. / Phan, A.T. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Bulges in left-handed G-quadruplexes. Authors: Das, P. / Ngo, K.H. / Winnerdy, F.R. / Maity, A. / Bakalar, B. / Mechulam, Y. / Schmitt, E. / Phan, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d5d.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d5d.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 7d5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d5d_validation.pdf.gz | 386 KB | Display | wwPDB validaton report |
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Full document | 7d5d_full_validation.pdf.gz | 386.4 KB | Display | |
Data in XML | 7d5d_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 7d5d_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/7d5d ftp://data.pdbj.org/pub/pdb/validation_reports/d5/7d5d | HTTPS FTP |
-Related structure data
Related structure data | 7d5eC 7d5fC 4u5mS 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: 8568.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.07 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.04 M sodium cacodylate trihydrate pH 6.0, 55% v/v -2-methyl-2,4-pentanediol and 0.012 M spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→27.33 Å / Num. obs: 20747 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 8.52 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.052 / Rrim(I) all: 0.135 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.182→1.224 Å / Rmerge(I) obs: 0.938 / Num. unique obs: 2060 / CC1/2: 0.5 / Rpim(I) all: 0.415 / Rrim(I) all: 1.028 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U5M Resolution: 1.18→27.33 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.724 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.04 / 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: 102.28 Å2 / Biso mean: 14.786 Å2 / Biso min: 5.13 Å2
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Refinement step | Cycle: final / Resolution: 1.18→27.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.182→1.212 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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