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

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General features for molecule PDB_00646
(click to expand/contract all tables)

Format:
Molecule ID [?]:PDB_00646
Molecule name [?]:CRYSTAL STRUCTURE OF THE WILD TYPE RIBOSOME FROM E. COLI, 50S SUBUNIT OF 70S RIBOSOME. THIS FILE, 1P
Source [?]:RCSB Protein Data Bank
Source ID [?]:1PNY
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 [?]: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 9.50 ANGSTROMS; ran through RNAview
Number of molecules [?]:2
Length [?]:2943
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: PDB_00644
Number of domains [?]:2
Number of unpaired bases [?]:1303
Number of paired bases [?]:1640

Click on any header below for additional features.

Stem features

Number of stems [?]:148
Number of base pairs in stems [?]:622
Maximum length of a stem [?]:18
Average length of a stem [?]:4.2
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-6.64
Minimum estimated free energy [?]:-22.9

Hairpin loop features

Number of hairpin loops [?]:59
Maximum number of free bases in hairpin loops [?]:15
Average number of free bases in hairpin loops [?]:5.95
Minimum number of free bases in hairpin loop [?]:2

Bulge loop features
Number of bulge loops [?]:21
Maximum number of free bases in bulge loops [?]:10
Average number of free bases in bulge loops [?]:1.21
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:52
Maximum number of free bases in internal loops:12
Average number of free bases in internal loops:2.62
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:6
Average internal loop absolute asymmetry:0.83
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.37
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:16
Maximum number of free bases in multi-loops:15
Average number of free bases in multi-loops:3.39
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:15
Average multi-loop absolute asymmetry:3.06
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:9
Average multi-loop relative asymmetry:1.18
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
Average number of branches in multi-loops:3.81
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 69
Total number of AA non-canonical base pairs:9
Total number of AC non-canonical base pairs:7
Total number of AG non-canonical base pairs:41
Total number of CC non-canonical base pairs:2
Total number of CU non-canonical base pairs:4
Total number of GG non-canonical base pairs:4
Total number of UU non-canonical base pairs:2

Pseudoknot features
Number of pseudoknots [?]:5
Number of bands:18
Number of base pairs in bands:198
Maximum band length:36
Average band length:11
Minimum band length:2
Maximum number of bands per pseudoknot:9
Average number of bands per pseudoknot:3.6
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:6
Average number of un-bands:1.4
Minimum number of un-bands:0
Maximum number of in-bands:23
Average number of in-bands:5.2
Minimum number of in-bands:0
Maximum number of unpaired bases:328
Average number of unpaired bases:84
Minimum number of unpaired bases:10
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:21
Maximum number of base pairs to remove, per pseudoknot:9
Average number of base pairs to remove, per pseudoknot:4.2
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:7
Maximum number of bands to remove, per pseudoknot:3
Average number of bands to remove, per pseudoknot:1.4
Minimum number of bands to remove, per pseudoknot:1



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