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

General features for molecule PDB_00029 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00029 Molecule name [?]: 23S RRNA STRUCTURE FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP AT 7.5 ANGSTROMS RESOLUTION Source [?]: RCSB Protein Data Bank Source ID [?]: 1C2W Reference [?]: F.MUELLER,I.SOMMER,P.BARANOV,R.MATADEEN,M.STOLDT, J.WOHNERT,M.GORLACH,M.VAN HEEL,R.BRIMACOMBE. THE 3D ARRANGEMENT OF THE 23 S AND 5 S RRNA IN THE ESCHERICHIA COLI 50 S RIBOSOMAL SUBUNIT BASED ON A CRYO-ELECTRON MICROSCOPIC RECONSTRUCTION AT 7.5 A RESOLUTION.. J.MOL.BIOL. V. 298 35 2000 ASTM JMOBAK UK ISSN 0022-2836 Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: ESCHERICHIA COLI Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-RAY, RESOLUTION 7.50 ANGSTROMS; ran through RNAview Number of molecules [?]: 1 Length [?]: 2904 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 1270 Number of paired bases [?]: 1634

Click on any header below for additional features.

Stem features Number of stems [?]: 147 Number of base pairs in stems [?]: 699 Maximum length of a stem [?]: 13 Average length of a stem [?]: 4.76 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.33 Minimum estimated free energy [?]: -18.7

Hairpin loop features Number of hairpin loops [?]: 60 Maximum number of free bases in hairpin loops [?]: 15 Average number of free bases in hairpin loops [?]: 5.48 Minimum number of free bases in hairpin loop [?]: 2

Bulge loop features Number of bulge loops [?]: 22 Maximum number of free bases in bulge loops [?]: 4 Average number of free bases in bulge loops [?]: 0.77 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: 12 Average number of free bases in internal loops: 3.75 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 10 Average internal loop absolute asymmetry: 1.5 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 6 Average internal loop relative asymmetry: 1.54 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 19 Maximum number of free bases in multi-loops: 20 Average number of free bases in multi-loops: 3.55 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 20 Average multi-loop absolute asymmetry: 3.44 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 20 Average multi-loop relative asymmetry: 1.29 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 7 Average number of branches in multi-loops: 3.84 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 6 Total number of AG non-canonical base pairs: 5 Total number of UU non-canonical base pairs: 1

Pseudoknot features Number of pseudoknots [?]: 5 Number of bands: 12 Number of base pairs in bands: 118 Maximum band length: 35 Average band length: 9.83 Minimum band length: 2 Maximum number of bands per pseudoknot: 3 Average number of bands per pseudoknot: 2.4 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 4 Average number of un-bands: 1.6 Minimum number of un-bands: 0 Maximum number of in-bands: 18 Average number of in-bands: 4.2 Minimum number of in-bands: 0 Maximum number of unpaired bases: 222 Average number of unpaired bases: 60.2 Minimum number of unpaired bases: 4 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 13 Maximum number of base pairs to remove, per pseudoknot: 4 Average number of base pairs to remove, per pseudoknot: 2.6 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 5 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

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