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(-) Description

Title :  TWO APO STRUCTURES OF THE ADENINE RIBOSWITCH APTAMER DOMAIN DETERMINED USING AN X-RAY FREE ELECTRON LASER
 
Authors :  J. R. Stagno, Y. -X. Wang, Y. Liu, Y. R. Bhandari, C. E. Conrad, G. Nelson, D. R. Wendel, T. A. White, A. Barty, R. A. Tuckey, N. A. Zatsepin, T. D. Gr P. Fromme, K. Tan, X. Ji, J. C. H. Spence
Date :  07 Oct 15  (Deposition) - 23 Nov 16  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Adenine Riboswitch, Purine Riboswitch, Apo, Ligand-Free, Rna, Gene Regulation, X-Ray Free Electron Laser (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Stagno, Y. Liu, Y. R. Bhandari, C. E. Conrad, S. Panja, M. Swain, L. Fan, G. Nelson, C. Li, D. R. Wendel, T. A. White, J. D. Coe, M. O. Wiedorn, J. Knoska, D. Oberthuer, R. A. Tuckey, P. Yu, M. Dyba, S. G. Tarasov, U. Weierstall, T. D. Grant, C. D. Schwieters, J. Zhang, A. R. Ferre-D'Amare, P. Fromme, D. E. Draper, M. Liang, M. S. Hunter, S. Boutet, K. Tan, X. Zuo, X. Ji, A. Barty, N. A. Zatsepin, H. N. Chapman, J. C. Spence, S. A. Woodson, Y. X. Wang
Structures Of Riboswitch Rna Reaction States By Mix-And-Inject Xfel Serial Crystallography.
Nature V. 541 242 2017
PubMed-ID: 27841871  |  Reference-DOI: 10.1038/NATURE20599

(-) Compounds

Molecule 1 - VIBRIO VULNIFICUS STRAIN 93U204 CHROMOSOME II, ADENINE RIBOSWITCH APTAMER DOMAIN
    ChainsA, B
    EngineeredYES
    Organism ScientificVIBRIO VULNIFICUS
    Organism Taxid672
    SyntheticYES

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG A:37 , HOH A:201 , HOH A:204 , U B:68 , HOH B:206 , HOH B:209binding site for residue MG A 101
2AC2SOFTWAREU A:51 , A A:52 , HOH A:202 , HOH A:203 , HOH B:203 , HOH B:205 , HOH B:208binding site for residue MG A 102
3AC3SOFTWAREU A:22 , A A:23 , U A:48binding site for residue MG A 103
4AC4SOFTWAREA B:24 , HOH B:201 , HOH B:202 , HOH B:207binding site for residue MG B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E54)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E54)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E54)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E54)

(-) Exons   (0, 0)

(no "Exon" information available for 5E54)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:65
                                                                                                
                  5e54 A 13 GGGAAGAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAU 77
                                    22        32        42        52        62        72     

Chain B from PDB  Type:RNA  Length:68
                                                                                                   
                  5e54 B 13 GGGAAGAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUCUU 80
                                    22        32        42        52        62        72        

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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)

(no "SCOP Domain" information available for 5E54)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E54)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E54)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5E54)

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 Related Entries

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