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

General features for molecule PDB_00643 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00643 Molecule name [?]: CRYSTAL STRUCTURE OF A STREPTOMYCIN DEPENDENT RIBOSOME FROM E. COLI, 30S SUBUNIT OF 70S RIBOSOME. TH Source [?]: RCSB Protein Data Bank Source ID [?]: 1PNS Reference [?]: A.VILA-SANJURJO,W.K.RIDGEWAY,V.SEYMANER,W.ZHANG, S.SANTOSO,K.YU,J.H.D.CATE. X-RAY CRYSTAL STRUCTURES OF THE WT AND A HYPER-ACCURATE RIBOSOME FROM ESCHERICHIA COLI. PROC.NATL.ACAD.SCI.USA V. 100 8682 2003 ASTM PNASA6 US ISSN 0027-8424 Type [?]: 16S 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 8.70 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 1688 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 9 Number of unpaired bases [?]: 548 Number of paired bases [?]: 1140

Click on any header below for additional features.

Stem features Number of stems [?]: 91 Number of base pairs in stems [?]: 499 Maximum length of a stem [?]: 23 Average length of a stem [?]: 5.49 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -8.87 Minimum estimated free energy [?]: -39.2

Hairpin loop features Number of hairpin loops [?]: 34 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 4.71 Minimum number of free bases in hairpin loop [?]: 2 Total number of UUCG hairpin motifs per molecule [?]: 2

Bulge loop features Number of bulge loops [?]: 27 Maximum number of free bases in bulge loops [?]: 3 Average number of free bases in bulge loops [?]: 0.74 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 17 Maximum number of free bases in internal loops: 8 Average number of free bases in internal loops: 2.41 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 2 Average internal loop absolute asymmetry: 1.06 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.65 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 12 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 2.82 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 7 Average multi-loop absolute asymmetry: 2.38 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 7 Average multi-loop relative asymmetry: 1.05 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.25 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 79 Total number of AA non-canonical base pairs: 12 Total number of AC non-canonical base pairs: 12 Total number of AG non-canonical base pairs: 42 Total number of CC non-canonical base pairs: 1 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: 7

Pseudoknot features Number of pseudoknots [?]: 4 Number of bands: 8 Number of base pairs in bands: 71 Maximum band length: 32 Average band length: 8.88 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: 2 Average number of un-bands: 0.5 Minimum number of un-bands: 0 Maximum number of in-bands: 9 Average number of in-bands: 3 Minimum number of in-bands: 0 Maximum number of unpaired bases: 62 Average number of unpaired bases: 29.5 Minimum number of unpaired bases: 15 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 10 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 2.5 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