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(-) Description

Title :  SELENIUM-ASSISTED NUCLEIC ACID CRYSTALLOGRAPHY: USE OF PHOSPHOROSELENOATES FOR MAD PHASING OF A DNA STRUCTURE
 
Authors :  C. J. Wilds, R. Pattanayek, C. Pan, Z. Wawrzak, M. Egli
Date :  14 Apr 05  (Deposition) - 19 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Left-Handed Z-Dna, Phosphoroselenoate, Multiwavelength Anomalous Dispersion (Mad), Covalent Modification Of Oligonucleotides, Oligonucleotide Analogue, Phasing Strategy, Synchrotron (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. J. Wilds, R. Pattanayek, C. Pan, Z. Wawrzak, M. Egli
Selenium-Assisted Nucleic Acid Crystallography: Use Of Phosphoroselenoates For Mad Phasing Of A Dna Structure
J. Am. Chem. Soc. V. 124 14910 2002
PubMed-ID: 12475332  |  Reference-DOI: 10.1021/JA021058B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*(GMS)P*CP*GP*CP*G)-3'
    ChainsA, B
    EngineeredYES
    Other DetailsSYNTHESIZED WITH A SOLID-PHASE OLIGONUCLEOTIDE SYNTHESIZER USING DNA PHOSPHORAMIDITES AND POTASSIUM SELENOCYANIDE FOR INTRODUCING THE PHOSPHOROSELENOATE LINKAGE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1GMS2Mod. Nucleotide2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3SPM1Ligand/IonSPERMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGMS A:2 , DC A:3 , DG A:6 , HOH A:401 , HOH A:408 , HOH A:438 , HOH A:458 , GMS B:108 , DG B:110 , DC B:111 , DG B:112 , HOH B:414 , HOH B:444BINDING SITE FOR RESIDUE SPM A 201
2AC2SOFTWAREDG B:112 , HOH B:418 , HOH B:420 , HOH B:431 , HOH B:437 , HOH B:439BINDING SITE FOR RESIDUE MG B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VRO)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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Chain A from PDB  Type:DNA  Length:6
                                      
                 1vro A   1 CgCGCG   6
                             |    
                             |    
                             2-GMS

Chain B from PDB  Type:DNA  Length:6
                                      
                 1vro B 107 CgCGCG 112
                             |    
                             |    
                           108-GMS

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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