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(-) Description

Title :  STRUCTURAL DISTORTIONS IN PSORALEN CROSS-LINKED DNA
 
Authors :  F. A. Hays, H. Yonggang, B. F. Eichman, W. Kong, J. Hearst, P. S. Ho
Date :  19 Sep 05  (Deposition) - 03 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Recombination, Psoralen, Nucleic Acid Structure, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. A. Hays, H. Yonggang, B. F. Eichman, W. Kong, J. Hearst, P. S. Ho
Structural Distortions In Psoralen Cross-Linked Dna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3'
    Chains: A, B
    Engineered: YES
    Other Details: THE D(CCGCTAGCGG) DECAMER DNA SEQUENCE WAS SYNTHESIZED USING- CYANOETHYL PHOSPHORAMIDITE CHEMISTRY ON AN APPLIED BIOSYSTEMS DNA SYNTHESIZER IN THE CENTER FOR GENE RESEARCH AND BIOTECHNOLOGY AT OREGON STATE UNIVERSITY. THE 5-O-DIMETHOXYTRITYL GROUP WAS LEFT ATTACHED TO FACILITATE SEPARATION FROM FAILURE SEQUENCES USING REVERSE-PHASE HPLC. THE TARGET FRACTION WAS THEN DRIED OVERNIGHT, DETRITYLATED USING 3% ACETIC ACID, DESALTED ON A SEPHADEX (SIGMA) G-25 SIZE EXCLUSION COLUMN AND DRIED OVERNIGHT.
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NA3Ligand/IonSODIUM ION
3PSO1Ligand/Ion4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN
4SPM1Ligand/IonSPERMINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3PSO2Ligand/Ion4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN
4SPM2Ligand/IonSPERMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC A:1 , DG A:10 , HOH A:177 , DG B:19 , HOH B:111 , HOH B:204BINDING SITE FOR RESIDUE SPM A 22
2AC2SOFTWAREDG A:9 , DG B:17 , HOH B:50 , HOH B:93 , HOH B:97 , HOH B:223BINDING SITE FOR RESIDUE CA B 23
3AC3SOFTWAREHOH A:33 , HOH A:57 , HOH A:70 , HOH A:151 , HOH A:166 , HOH A:180BINDING SITE FOR RESIDUE NA A 24
4AC4SOFTWAREHOH A:42 , HOH A:90 , HOH A:224 , HOH B:75BINDING SITE FOR RESIDUE CA A 25
5AC5SOFTWAREHOH A:36 , HOH A:53 , HOH A:126 , HOH A:142 , HOH B:48BINDING SITE FOR RESIDUE NA B 26
6AC6SOFTWAREDC A:4 , HOH A:29 , HOH A:141 , DT B:15BINDING SITE FOR RESIDUE NA A 27
7AC7SOFTWAREDC A:4 , DT A:5 , DA A:6 , DT B:15 , DA B:16BINDING SITE FOR RESIDUE PSO A 21

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B2B)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:DNA  Length:10
                                         
                  2b2b A  1 CCGCTAGCGG 10
                                    10


Chain B from PDB  Type:DNA  Length:10
                                         
                  2b2b B 11 CCGCTAGCGG 20
                                    20
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2B2B)

(-) CATH Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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(-) Related Entries Specified in the PDB File

1fhy PSORALEN CROSS-LINKED D(CCGCTAGCGG) FORMS HOLLIDAY JUNCTION