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

General features for molecule PDB_00458 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00458 Molecule name [?]: CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS IN COMPLEX WITH THE TRANSLA Source [?]: RCSB Protein Data Bank Source ID [?]: 1I96 Reference [?]: M.PIOLETTI,F.SCHLUNZEN,J.HARMS,R.ZARIVACH, M.GLUHMANN,H.AVILA,A.BASHAN,H.BARTELS,T.AUERBACH, C.JACOBI,T.HARTSCH,A.YONATH,F.FRANCESCHI. CRYSTAL STRUCTURES OF COMPLEXES OF THE SMALL RIBOSOMAL SUBUNIT WITH TETRACYCLINE, EDEINE AND IF3.. EMBO J. V. 20 1829 2001 ASTM EMJODG UK ISSN 0261-4189 Type [?]: 16S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: THERMUS THERMOPHILUS Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 4.20 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 1514 Fragments used [?]: Yes Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00456, PDB_00457, PDB_00459 Number of domains [?]: 4 Number of unpaired bases [?]: 516 Number of paired bases [?]: 998

Click on any header below for additional features.

Stem features Number of stems [?]: 86 Number of base pairs in stems [?]: 432 Maximum length of a stem [?]: 14 Average length of a stem [?]: 5.03 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.23 Minimum estimated free energy [?]: -26.1

Hairpin loop features Number of hairpin loops [?]: 28 Maximum number of free bases in hairpin loops [?]: 14 Average number of free bases in hairpin loops [?]: 4.61 Minimum number of free bases in hairpin loop [?]: 2 Total number of UUCG hairpin motifs per molecule [?]: 1

Bulge loop features Number of bulge loops [?]: 23 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.72 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 23 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.43 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1.04 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.61 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 11 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 3.09 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.26 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.12 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.18 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 60 Total number of AA non-canonical base pairs: 8 Total number of AC non-canonical base pairs: 10 Total number of AG non-canonical base pairs: 31 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 4 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 67 Maximum band length: 35 Average band length: 8.38 Minimum band length: 2 Maximum number of bands per pseudoknot: 2 Average number of bands per pseudoknot: 2 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 3 Average number of un-bands: 1.25 Minimum number of un-bands: 0 Maximum number of in-bands: 9 Average number of in-bands: 2.5 Minimum number of in-bands: 0 Maximum number of unpaired bases: 58 Average number of unpaired bases: 27 Minimum number of unpaired bases: 9 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 11 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.75 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 4 Maximum number of bands to remove, per pseudoknot: 1 Average number of bands to remove, per pseudoknot: 1 Minimum number of bands to remove, per pseudoknot: 1