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Yorodumi- PDB-1rrd: DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rrd | ||||||
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Title | DNA/RNA HYBRID DUPLEX CONTAINING A PURINE-RICH RNA STRAND, NMR, 10 STRUCTURES | ||||||
Components |
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Keywords | DNA-RNA HYBRID / DNA/RNA HYBRID / PURINE/PYRIMIDINE-RICH STRANDS / ANTISENSE | ||||||
Function / homology | DNA / RNA Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Gyi, J.I. / Lane, A.N. / Conn, G.L. / Brown, T. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes. Authors: Gyi, J.I. / Lane, A.N. / Conn, G.L. / Brown, T. #1: Journal: Biochemistry / Year: 1996 Title: Comparison of the Thermodynamic Stabilities and Solution Conformations of DNA.RNA Hybrids Containing Purine-Rich and Pyrimidine-Rich Strands with DNA and RNA Duplexes Authors: Gyi, J.I. / Conn, G.L. / Lane, A.N. / Brown, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rrd.cif.gz | 130 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rrd.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 1rrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rrd_validation.pdf.gz | 330.6 KB | Display | wwPDB validaton report |
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Full document | 1rrd_full_validation.pdf.gz | 409.7 KB | Display | |
Data in XML | 1rrd_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1rrd_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/1rrd ftp://data.pdbj.org/pub/pdb/validation_reports/rr/1rrd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 3287.076 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 2961.940 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 7.0 / Temperature: 303 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software | Name: AMBER / Classification: refinement | ||||||||||||||||||||||||
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NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: DISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, PENTOSE PSEUDOROTATIONAL PHASE ANGLES/AMPLITUDES AND FRACTION OF SOUTH STATE SUGARS CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING ...Details: DISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, PENTOSE PSEUDOROTATIONAL PHASE ANGLES/AMPLITUDES AND FRACTION OF SOUTH STATE SUGARS CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING CONSTANTS BY A LEAST-SQUARES/GRID SEARCH METHOD IMPLEMENTED IN NUCFIT AND PFIT (A.N. LANE, NIMR, UK). TEN DIFFERENT SETS OF UNIQUE RESTRAINTS GENERATED 10 STRUCTURES, THE AVERAGE OF WHICH SATISFIED THE EXPERIMENTALLY DERIVED FRACTION OF SOUTH STATE SUGARS BETTER STRUCTURES GENERATED FROM A SINGLE SET OF RESTRAINTS. INTERNU CLEOTIDE DISTANCE CONSTRAINTS CALCULATED FROM NOE-BUILD-UP CURVES. STRUCTURES CALCULATED BY SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER 95.0 USING AN AMBER FORCE FIELD AND A DISTANCE DIELECTRIC CONSTANT. | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST POTENTIAL ENERGY, MINIMAL VIOLATIONS AND ACCEPTABLE STEREOCHEMISTRY Conformers calculated total number: 100 / Conformers submitted total number: 10 |