+Open data
-Basic information
Entry | Database: PDB / ID: 1k9g | ||||||||||||||||||
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Title | Crystal Structure of the Complex of Cryptolepine-d(CCTAGG)2 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DNA intercalator complex | Function / homology | 5-METHYL-5H-INDOLO[3,2-B]QUINOLINE / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | Authors | Lisgarten, J.N. / Coll, M. / Portugal, J. / Wright, C.W. / Aymami, J. | Citation | Journal: Nat.Struct.Biol. / Year: 2002 | Title: The antimalarial and cytotoxic drug cryptolepine intercalates into DNA at cytosine-cytosine sites. Authors: Lisgarten, J.N. / Coll, M. / Portugal, J. / Wright, C.W. / Aymami, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k9g.cif.gz | 14.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k9g.ent.gz | 8.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k9g ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k9g | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The double helix is generated by the operation -x,-y+2,z. |
-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.76 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Magnesium acetate, MES, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 3543 / Num. obs: 3356 / % possible obs: 87.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / Num. unique all: 292 / % possible all: 73.2 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS Highest resolution: 1.4 Å / % possible obs: 73.2 % / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.208 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |