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Yorodumi- PDB-1r4e: Solution structure of the Complex Formed between a Left-Handed We... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r4e | ||||||
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Title | Solution structure of the Complex Formed between a Left-Handed Wedge-Shaped Spirocyclic Molecule and Bulged DNA | ||||||
Components |
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Keywords | DNA / Wedge-shaped spirocyclic enantiomer-bulged DNA complex | ||||||
Function / homology | Chem-DDI / DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing | ||||||
Authors | Hwang, G.S. / Jones, G.B. / Goldberg, I.H. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Stereochemical control of small molecule binding to bulged DNA: comparison of structures of spirocyclic enantiomer-bulged DNA complexes. Authors: Hwang, G.S. / Jones, G.B. / Goldberg, I.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r4e.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r4e.ent.gz | 147.6 KB | Display | PDB format |
PDBx/mmJSON format | 1r4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r4e_validation.pdf.gz | 412.4 KB | Display | wwPDB validaton report |
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Full document | 1r4e_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 1r4e_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 1r4e_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r4e ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r4e | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 4265.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by DNA synthesizer. |
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#2: DNA chain | Mass: 3694.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by DNA synthesizer. |
#3: Chemical | ChemComp-DDI / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using 2D homonuclear and heteronuclear techniques. |
-Sample preparation
Details | Contents: 1.2 mM ent-DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer, 90% H2O/10% D2O, 99.96% D2O Solvent system: 90% H2O/10% D2O; 99.96% D2O |
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Sample conditions | Ionic strength: 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 427 NOE restraints and 166 dihedral angle restraints. | ||||||||||||||||
NMR representative | Selection criteria: all calculated structures submited have the least restraint violation and the lowst energy. | ||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 10 / Conformers submitted total number: 10 |