+Open data
-Basic information
Entry | Database: PDB / ID: 139d | ||||||||||||||||||
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Title | SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-QUADRUPLEX / ANTI GLYCOSIDIC TORSION ANGLES | Function / homology | DNA | Function and homology information Method | SOLUTION NMR / DISTANCE GEOMETRY, MOLECULAR DYNAMICS | Authors | Patel, D.J. / Wang, Y. | Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Solution structure of a parallel-stranded G-quadruplex DNA. Authors: Wang, Y. / Patel, D.J. #1: Journal: Biochemistry / Year: 1992 Title: Guanine Residues in D(T2Ag3) and D(T2G4) Form Parallel-Stranded Potassium Cation Stabilized G-Quadruplexes with Anti Glycosidic Torsion Angles in Solution Authors: Wang, Y. / Patel, D.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 139d.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb139d.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 139d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 139d_validation.pdf.gz | 329 KB | Display | wwPDB validaton report |
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Full document | 139d_full_validation.pdf.gz | 379.3 KB | Display | |
Data in XML | 139d_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 139d_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/39/139d ftp://data.pdbj.org/pub/pdb/validation_reports/39/139d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 2184.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-Processing
Software |
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NMR software | Name: X-PLOR / Developer: BRUNGER / Classification: refinement | ||||||||
Refinement | Method: DISTANCE GEOMETRY, MOLECULAR DYNAMICS / Software ordinal: 1 Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ON A MOLECULAR MODEL BUILT TO QUALITATIVELY FIT THE NMR DATA. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SEVEN ...Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ON A MOLECULAR MODEL BUILT TO QUALITATIVELY FIT THE NMR DATA. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SEVEN STRUCTURES WERE CALCULATED USING DISTANCE RESTRAINTS (WITH DIFFERENT SEEDS FOR INITIAL VELOCITY ASSIGNMENTS). IN THE SECOND STAGE, FOUR OF THE SEVEN DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER BY NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS CALCULATIONS. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THE SECOND STAGE. THE FINAL R(1/6) VALUES FOR THE FOUR AVERAGED MINIMIZED STRUCTURES WERE BETWEEN 0.025 AND 0.033. RMS DEVIATIONS FROM IDEALIZED GEOMETRY FOR THE TWO AVERAGED MINIMIZED STRUCTURES ARE AS FOLLOWS: MODEL1 MODEL2 MODEL3 MODEL4 BOND (ANGSTROMS) 0.013 0.013 0.012 0.011 ANGLES (DEGREES) 2.713 2.634 2.731 2.728 IMPROPERS (DEGREES) 0.476 0.560 0.242 0.280. THE STRUCTURE HAS AN APPROXIMATE FOUR-FOLD SYMMETRY RELATING THE FOUR STRANDS WITH THE SYMMETRY AXIS COINCIDENT WITH THE HELICAL AXIS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. IT WILL ALSO YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *B* AND WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *D* WHEN APPLIED TO CHAIN *C*. | ||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 7 / Conformers submitted total number: 4 |