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Yorodumi- PDB-1byx: CHIMERIC HYBRID DUPLEX R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1byx | ||||||
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Title | CHIMERIC HYBRID DUPLEX R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE TRNA-DNA JUNCTION FORMED DURING INITIATION OF HIV-1 REVERSE TRANSCRIPTION | ||||||
Components |
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Keywords | DNA-RNA HYBRID / RNA:RNA-DNA CHIMERIC HYBRID / RNASE H / REVERSE TRANSCRIPTASE / DNA-RNA COMPLEX | ||||||
Function / homology | DNA/RNA hybrid / RNA Function and homology information | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Authors | Szyperski, T. / Goette, M. / Billeter, M. / Perola, E. / Cellai, L. | ||||||
Citation | Journal: J.Biomol.NMR / Year: 1999 Title: NMR structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription. Authors: Szyperski, T. / Gotte, M. / Billeter, M. / Perola, E. / Cellai, L. / Heumann, H. / Wuthrich, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1byx.cif.gz | 205.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1byx.ent.gz | 168.6 KB | Display | PDB format |
PDBx/mmJSON format | 1byx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1byx_validation.pdf.gz | 340.6 KB | Display | wwPDB validaton report |
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Full document | 1byx_full_validation.pdf.gz | 540.4 KB | Display | |
Data in XML | 1byx_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1byx_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1byx ftp://data.pdbj.org/pub/pdb/validation_reports/by/1byx | 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: RNA chain | Mass: 2581.601 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE RNA:RNA-DNA CHIMERIC HYBRID DUPLEX WAS CHEMICALLY SYNTHESIZED FROM THE HUMAN IMMUNODIFICIENCY VIRUS TYPE 1 (HIV-1). THE DUPLEX IS FORMED DURING THE INITIATION OF (-)DNA STRAND SYNTHESIS IN HIV-1 REPLICATION. |
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#2: DNA/RNA hybrid | Mass: 2451.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHIMERIC HYBRID RNA/RNA-DNA DUPLEX |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE 20 STRUCTURES ARE ENERGY-MINIMIZED WITH THE AMBER FORCE FIELD USING THE PROGRAM OPAL |
-Sample preparation
Sample conditions | pH: 7 / Pressure: 1 atm / Temperature: 298 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 Details: REFINEMENT DETAILS ARE DESCRIBED IN THE JRNL CITATION ABOVE | |||||||||
NMR ensemble | Conformer selection criteria: DYANA TARGET FUNCTION / Conformers calculated total number: 100 / Conformers submitted total number: 20 |