RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database

General features for molecule PDB_00833 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00833 Molecule name [?]: RRF DOMAIN I IN COMPLEX WITH THE 50S RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS Source [?]: RCSB Protein Data Bank Source ID [?]: 1Y69 Reference [?]: D.N.WILSON,F.SCHLUENZEN,J.M.HARMS,T.YOSHIDA, T.OHKUBO,R.ALBRECHT,J.BUERGER,Y.KOBAYASHI,P.FUCINI. X-RAY CRYSTALLOGRAPHY ON RIBOSOME RECYCLING: MECHANISM OF BINDING AND ACTION OF RRF ON THE 50S RIBOSOMAL SUBUNIT. EMBO J. V. 24 251 2005 ASTM EMJODG UK ISSN 0261-4189 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: DEINOCOCCUS RADIODURANS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 3.33 ANGSTROMS; ran through RNAview Number of molecules [?]: 2 Length [?]: 2884 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00609, PDB_00615, PDB_00616, PDB_00719, PDB_00808 Number of domains [?]: 2 Number of unpaired bases [?]: 1246 Number of paired bases [?]: 1638

Click on any header below for additional features.

Stem features Number of stems [?]: 141 Number of base pairs in stems [?]: 612 Maximum length of a stem [?]: 12 Average length of a stem [?]: 4.34 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.77 Minimum estimated free energy [?]: -22.9

Hairpin loop features Number of hairpin loops [?]: 58 Maximum number of free bases in hairpin loops [?]: 15 Average number of free bases in hairpin loops [?]: 5.84 Minimum number of free bases in hairpin loop [?]: 0

Bulge loop features Number of bulge loops [?]: 21 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.76 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 46 Maximum number of free bases in internal loops: 8 Average number of free bases in internal loops: 2.47 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 0.85 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.43 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 16 Maximum number of free bases in multi-loops: 23 Average number of free bases in multi-loops: 3.88 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 22 Average multi-loop absolute asymmetry: 3.89 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 23 Average multi-loop relative asymmetry: 1.4 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 3.75 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 73 Total number of AA non-canonical base pairs: 5 Total number of AC non-canonical base pairs: 11 Total number of AG non-canonical base pairs: 38 Total number of CC non-canonical base pairs: 4 Total number of CU non-canonical base pairs: 9 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 3

Pseudoknot features Number of pseudoknots [?]: 6 Number of bands: 20 Number of base pairs in bands: 207 Maximum band length: 35 Average band length: 10.35 Minimum band length: 2 Maximum number of bands per pseudoknot: 9 Average number of bands per pseudoknot: 3.33 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 7 Average number of un-bands: 1.5 Minimum number of un-bands: 0 Maximum number of in-bands: 23 Average number of in-bands: 4.17 Minimum number of in-bands: 0 Maximum number of unpaired bases: 311 Average number of unpaired bases: 69 Minimum number of unpaired bases: 8 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 24 Maximum number of base pairs to remove, per pseudoknot: 10 Average number of base pairs to remove, per pseudoknot: 4 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 8 Maximum number of bands to remove, per pseudoknot: 3 Average number of bands to remove, per pseudoknot: 1.33 Minimum number of bands to remove, per pseudoknot: 1

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