+Open data
-Basic information
Entry | Database: PDB / ID: 1l1h | ||||||||||||||||||
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Title | Crystal Structure of the Quadruplex DNA-Drug Complex | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / G-Quadruplex / Oxytricha / four-stranded DNA | Function / homology | : / Chem-PYN / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | Authors | Haider, S.M. / Parkinson, G.N. / Neidle, S. | Citation | Journal: J.Mol.Biol. / Year: 2003 | Title: Structure of a G-quadruplex-Ligand Complex Authors: Haider, S.M. / Parkinson, G.N. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l1h.cif.gz | 27.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l1h.ent.gz | 18.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l1h_validation.pdf.gz | 591.4 KB | Display | wwPDB validaton report |
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Full document | 1l1h_full_validation.pdf.gz | 594 KB | Display | |
Data in XML | 1l1h_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1l1h_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/1l1h ftp://data.pdbj.org/pub/pdb/validation_reports/l1/1l1h | HTTPS FTP |
-Related structure data
Related structure data | 1jpqS S: Starting model for refinement |
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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: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The sequence is naturally found in Oxytricha nova. #2: Chemical | ChemComp-PYN / | #3: Chemical | ChemComp-K / #4: Water | ChemComp-HOH / | |
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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: 2.03 Å3/Da / Density % sol: 39.34 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 12 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 6, 2002 |
Radiation | Monochromator: Copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→10 Å / Num. all: 6932 / Num. obs: 6932 / % possible obs: 94.04 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 13.8 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 6540 / % possible obs: 94 % / Redundancy: 3.8 % / Num. measured all: 24883 |
Reflection shell | *PLUS % possible obs: 96.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JPQ Resolution: 1.75→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.75→10 Å
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 6540 / Rfactor Rfree: 0.2245 / Rfactor Rwork: 0.1511 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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