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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SPECIFICITY DOMAIN OF RIBONUCLEASE P RNA
 
Authors :  A. S. Krasilnikov, X. Yang, T. Pan, A. Mondragon
Date :  03 Dec 02  (Deposition) - 18 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribonuclease P Rna, P Rna, S-Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Krasilnikov, X. Yang, T. Pan, A. Mondragon
Crystal Structure Of The Specificity Domain Of Ribonuclease P
Nature V. 421 760 2003
PubMed-ID: 12610630  |  Reference-DOI: 10.1038/NATURE01386
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE P RNA
    Chains: A, B
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PUC19
    Expression System Taxid: 1423
    Fragment: SPECIFICITY-DOMAIN, S-DOMAIN
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Other Details: THE RNA WAS PRODUCED BY VITRO TRANSCRIPTION WITH T7 POLYMERASE FROM A PUC19-BASED TEMPLATE WHICH CONTAINED CLONED SEQUENCE OF THE S-DOMAIN.

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 35)

Asymmetric Unit (2, 35)
No.NameCountTypeFull Name
1MG12Ligand/IonMAGNESIUM ION
2PB23Ligand/IonLEAD (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PB-1Ligand/IonLEAD (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PB-1Ligand/IonLEAD (II) ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREC A:134BINDING SITE FOR RESIDUE MG A 6
02AC2SOFTWAREA A:230 , PB A:242BINDING SITE FOR RESIDUE MG A 7
03AC3SOFTWAREU B:165 , A B:167BINDING SITE FOR RESIDUE MG B 241
04AC4SOFTWAREA B:106 , G B:107BINDING SITE FOR RESIDUE MG B 242
05AC5SOFTWAREA B:191BINDING SITE FOR RESIDUE MG B 244
06AC6SOFTWAREA B:135 , G B:226BINDING SITE FOR RESIDUE MG B 245
07AC7SOFTWAREG B:193BINDING SITE FOR RESIDUE MG B 246
08AC8SOFTWAREU A:174BINDING SITE FOR RESIDUE MG B 247
09AC9SOFTWAREC A:186 , G A:219 , G A:220BINDING SITE FOR RESIDUE PB A 241
10BC1SOFTWAREMG A:7 , G A:132BINDING SITE FOR RESIDUE PB A 242
11BC2SOFTWAREG A:86BINDING SITE FOR RESIDUE PB A 243
12BC3SOFTWAREC A:134 , U A:181 , G A:182BINDING SITE FOR RESIDUE PB A 244
13BC4SOFTWAREC A:102BINDING SITE FOR RESIDUE PB A 245
14BC5SOFTWAREG A:219BINDING SITE FOR RESIDUE PB A 246
15BC6SOFTWAREG A:136BINDING SITE FOR RESIDUE PB A 248
16BC7SOFTWAREU A:228 , A A:231BINDING SITE FOR RESIDUE PB A 249
17BC8SOFTWAREG A:168BINDING SITE FOR RESIDUE PB A 250
18BC9SOFTWAREG A:97BINDING SITE FOR RESIDUE PB A 251
19CC1SOFTWAREG A:86BINDING SITE FOR RESIDUE PB A 252
20CC2SOFTWAREC B:186BINDING SITE FOR RESIDUE PB B 301
21CC3SOFTWAREG B:90 , G B:132BINDING SITE FOR RESIDUE PB B 302
22CC4SOFTWAREG B:86BINDING SITE FOR RESIDUE PB B 303
23CC5SOFTWAREA B:160 , G B:163BINDING SITE FOR RESIDUE PB B 304
24CC6SOFTWAREC B:134 , U B:181 , G B:182BINDING SITE FOR RESIDUE PB B 305
25CC7SOFTWAREU B:101 , C B:102 , U B:104BINDING SITE FOR RESIDUE PB B 306
26CC8SOFTWAREG B:219BINDING SITE FOR RESIDUE PB B 307
27CC9SOFTWAREA B:231BINDING SITE FOR RESIDUE PB B 310
28DC1SOFTWAREG B:97BINDING SITE FOR RESIDUE PB B 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NBS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NBS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NBS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NBS)

(-) Exons   (0, 0)

(no "Exon" information available for 1NBS)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:RNA  Length:120
                                                                                                                                                        
                 1nbs A  86 GCGAGCCUAGCGAAGUCAUAAGCUAGGGCAGUCUUUAGAGGCUGACGGCAGGAAAAAGAGUAUCCUUGAAAGUGCCACAGUGACGAAGUCUCGAGAGUGGAACGCGGUAAACCCCUCGCA 240
                                    95       105       115       125       135      |168       178       188       198 ||    220       230       240
                                                                                  142|                               200|                           
                                                                                   166                                213                           


Chain B from PDB  Type:RNA  Length:150
                                                                                                                                                                                      
                 1nbs B  86 GCGAGCCUAGCGAAGUCAUAAGCUAGGGCAGUCUUGGCUGACGGCAGGAAAAAAGCCUACGUCUUCGGAUAUGGCUGAGUAUCCUUGAAAGUGCCACAGUGACGAAGUCUCACUAGAAAUGGUGAGAGUGGAACGCGGUAAACCCCUCGC 239
                                    95       105       115    || 129       139       149       159       169       179       189       199       209       219       229       239
                                                            120|                                                                                                                  
                                                             125
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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(-) Related Entries Specified in the PDB File

1nxl MODEL WHICH IS COMPOSED OF THE TWO MOLECULES IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT AND REPRESENTS ENTIRE SPECIFICITY DOMAIN OF RIBONUCLEASE P RNA