[English] 日本語
Yorodumi- PDB-156d: REFINED SOLUTION STRUCTURE OF THE DIMERIC QUADRUPLEX FORMED FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 156d | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | REFINED SOLUTION STRUCTURE OF THE DIMERIC QUADRUPLEX FORMED FROM THE OXYTRICHA TELOMERIC OLIGONUCLEOTIDE D(GGGGTTTTGGGG) | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / QUADRUPLEX / OXYTRICHA TELOMERIC OLIGONUCLEOTIDE D(GGGGTTTTGGGG) | Function / homology | DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / SUBSTRUCTURE EMBEDDING, SIMULATED ANNEALING, MATRIX RELAXATION | Model type details | minimized average | Authors | Schultze, P. / Smith, F.W. / Feigon, J. | Citation | Journal: Structure / Year: 1994 Title: Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG). Authors: Schultze, P. / Smith, F.W. / Feigon, J. #1: Journal: Biochemistry / Year: 1993 Title: Strand Orientation in the DNA Quadruplex Formed from the Oxytricha Telomere Repeat Oligonucleotide D(G4T4G4) in Solution Authors: Smith, F.W. / Feigon, J. #2: Journal: Nature / Year: 1992 Title: Quadruplex Structure of Oxytricha Telomeric DNA Oligonucleotides Authors: Smith, F.W. / Feigon, J. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 156d.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb156d.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 156d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 156d_validation.pdf.gz | 311.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 156d_full_validation.pdf.gz | 392.7 KB | Display | |
Data in XML | 156d_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 156d_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/56/156d ftp://data.pdbj.org/pub/pdb/validation_reports/56/156d | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|
-Sample preparation
Details | Solvent system: H2O/D20 |
---|---|
Sample | Conc.: 0.0052 M / Component: SODIUM CHLORIDE |
Sample conditions | Ionic strength: .05M / pH: 6 / Temperature units: K |
Crystal grow | *PLUS Method: other / Details: NMR |
-Processing
Software |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
NMR software | Name: X-PLOR / Developer: BRUNGER / Classification: refinement | ||||||||
Refinement | Method: SUBSTRUCTURE EMBEDDING, SIMULATED ANNEALING, MATRIX RELAXATION Software ordinal: 1 Details: REFINEMENT PROCEDURE STEP (1) SUBSTRUCTURE EMBEDDING ON 20 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY SIMULATED ANNEALING (20 STRUCTURES) STEP (3) SIMULATED ANNEALING AND ...Details: REFINEMENT PROCEDURE STEP (1) SUBSTRUCTURE EMBEDDING ON 20 STRUCTURES STEP (2) TEMPLATE FITTING AND REGULARIZATION BY SIMULATED ANNEALING (20 STRUCTURES) STEP (3) SIMULATED ANNEALING AND ENERGY MINIMIZATION (20 STRUCTURES) STEP (4) RELAXATION MATRIX REFINEMENT ON THE BEST 8 OF 20 STRUCTURES. THE DIMER POSSESSES A TWO-FOLD AXIS OF SYMMETRY. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 1 WHEN APPLIED TO CHAIN A OF MODEL 1. THE COORDINATES OF THE ATOMS OF CHAIN A TRANSFORMED IN THIS MANNER HAVE AN RMSD OF 0.0015 ANGSTROMS FROM THE COORDINATES OF CHAIN B GIVEN IN THIS ENTRY. | ||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 20 / Conformers submitted total number: 8 |