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(-) Description

Title :  RIP-RADIATION-DAMAGE INDUCED PHASING
 
Authors :  R. B. G. Ravelli, H. -K. S. Leiros, B. Pan, M. Caffrey, S. Mcsweeney
Date :  13 Nov 02  (Deposition) - 04 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Dna, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. B. G. Ravelli, H. -K. S. Leiros, B. Pan, M. Caffrey, S. Mcsweeney
Specific Radiation-Damage Can Be Used To Solve Macromolecular Crystal Structures
Structure V. 11 217 2003
PubMed-ID: 12575941  |  Reference-DOI: 10.1016/S0969-2126(03)00006-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA/DNA (5'-R(*U)-D(P*(BGM))-R(P*AP*GP*GP*U)-3')
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Other Details: THE RNA HEXAMER UGAGGU WHERE THE 2ND G WAS REPLACED BY A C8-BROMINATED GD WAS PHASED USING RADIATION DAMAGE ON THE HIGHLY SUSCEPTIBLE BR-C8 BOND.
    Other Details - Source: THE DNA/RNA HYBRID WAS SYNTHESIZED BY THE PHOSPHORAMIDITE METHOD USING AN APPLIED BIOSYSTEM DNA SYNTHESIZER 391
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1BGM8Mod. Nucleotide8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
2K9Ligand/IonPOTASSIUM ION
3SPM2Ligand/IonSPERMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG B:5 , U B:6 , K B:102 , G E:5 , U E:6 , G F:5 , U F:6 , G G:5 , U G:6BINDING SITE FOR RESIDUE K B 101
02AC2SOFTWAREG B:4 , G B:5 , K B:101 , K B:107 , G E:4 , G E:5 , G F:4 , G F:5 , G G:4 , G G:5BINDING SITE FOR RESIDUE K B 102
03AC3SOFTWAREG A:5 , U A:6 , K A:104 , G C:5 , U C:6 , G D:5 , U D:6 , G H:5 , U H:6BINDING SITE FOR RESIDUE K A 103
04AC4SOFTWAREG A:4 , G A:5 , K A:103 , K A:109 , G C:4 , G C:5 , G D:4 , G D:5 , G H:4 , G H:5BINDING SITE FOR RESIDUE K A 104
05AC5SOFTWAREBGM A:2 , K A:108 , BGM B:2 , BGM C:2 , BGM D:2 , BGM E:2 , K E:106 , BGM F:2 , BGM G:2 , BGM H:2BINDING SITE FOR RESIDUE K A 105
06AC6SOFTWAREK A:105 , BGM B:2 , A B:3 , K B:107 , BGM E:2 , A E:3 , BGM F:2 , A F:3 , BGM G:2 , A G:3BINDING SITE FOR RESIDUE K E 106
07AC7SOFTWAREA B:3 , G B:4 , K B:102 , A E:3 , G E:4 , K E:106 , A F:3 , G F:4 , A G:3 , G G:4BINDING SITE FOR RESIDUE K B 107
08AC8SOFTWAREBGM A:2 , A A:3 , K A:105 , K A:109 , BGM C:2 , A C:3 , BGM D:2 , A D:3 , BGM H:2 , A H:3BINDING SITE FOR RESIDUE K A 108
09AC9SOFTWAREA A:3 , G A:4 , K A:104 , K A:108 , A C:3 , G C:4 , A D:3 , G D:4 , A H:3 , G H:4BINDING SITE FOR RESIDUE K A 109
10BC1SOFTWAREA D:3 , G D:4 , A F:3 , BGM H:2 , HOH H:234 , HOH H:331BINDING SITE FOR RESIDUE SPM H 501
11BC2SOFTWAREBGM A:2 , A A:3 , BGM B:2 , A B:3 , HOH B:269 , HOH C:263 , HOH C:309 , BGM D:2 , A D:3 , HOH D:341 , BGM E:2 , A E:3BINDING SITE FOR RESIDUE SPM B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N7A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N7A)

(-) Exons   (0, 0)

(no "Exon" information available for 1N7A)

(-) Sequences/Alignments

Asymmetric/Biological 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
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Chain A from PDB  Type:DNA/RNA  Length:6
                                    
                   1n7a A 1 UgAGGU 6
                             |    
                             |    
                             2-BGM


Chain B from PDB  Type:DNA/RNA  Length:6
                                    
                   1n7a B 1 UgAGGU 6
                             |    
                             2-BGM


Chain C from PDB  Type:DNA/RNA  Length:6
                                    
                   1n7a C 1 UgAGGU 6
                             |    
                             2-BGM


Chain D from PDB  Type:DNA/RNA  Length:6
                                    
                   1n7a D 1 UgAGGU 6
                             |    
                             2-BGM


Chain E from PDB  Type:DNA/RNA  Length:6
                                    
                   1n7a E 1 UgAGGU 6
                             |    
                             2-BGM


Chain F from PDB  Type:DNA/RNA  Length:6
                                    
                   1n7a F 1 UgAGGU 6
                             |    
                             2-BGM


Chain G from PDB  Type:DNA/RNA  Length:6
                                    
                   1n7a G 1 UgAGGU 6
                             |    
                             2-BGM


Chain H from PDB  Type:DNA/RNA  Length:6
                                    
                   1n7a H 1 UgAGGU 6
                             |    
                             2-BGM
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1N7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1N7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1N7A)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1N7A)

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  1n7a
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1n6x TRYPSIN MODEL REFINED AGAINST DATA COLLECTED BEFORE "X-RAY BURN"
1n6y TRYPSIN MODEL REFINED AGAINST DATA COLLECTED AFTER "X-RAY BURN"
1n7b RNA/DNA MODEL REFINED AGAINST DATA COLLECTED AFTER "X-RAY BURN"