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- PDB-103d: THE UNUSUAL STRUCTURE OF THE HUMAN CENTROMERE (GGA)2 MOTIF: UNPAI... -

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Basic information

Entry
Database: PDB / ID: 103d
TitleTHE UNUSUAL STRUCTURE OF THE HUMAN CENTROMERE (GGA)2 MOTIF: UNPAIRED GUANOSINE RESIDUES STACKED BETWEEN SHEARED G(DOT)A PAIRS
ComponentsDNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
KeywordsDNA / DOUBLE HELIX / G-G STACKING / G:A MISMATCH / HUMAN CENTROMERE REPEAT / GA-BRACKETED G-STACK MOTIF
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsChou, S.-H. / Zhu, L. / Reid, B.R.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: The unusual structure of the human centromere (GGA)2 motif. Unpaired guanosine residues stacked between sheared G.A pairs.
Authors: Chou, S.H. / Zhu, L. / Reid, B.R.
History
DepositionDec 16, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
B: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,5032
Polymers7,5032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: DNA chain DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')


Mass: 3751.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

SoftwareName: AMBER / Classification: refinement
NMR softwareName: Discover / Developer: BIOSYM TECHNOLOGIES, INC. / Classification: refinement
RefinementSoftware ordinal: 1
Details: R VALUE 0.250 FINAL RMS COORD. SHIFT 0.65 ANGSTROMS NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 772 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF ...Details: R VALUE 0.250 FINAL RMS COORD. SHIFT 0.65 ANGSTROMS NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 772 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0. THE DUPLEX CONTAINS UNPAIRED STAGGERED GUANOSINE RESIDUES, WHICH CO-STACK BY INTERCALATION BETWEEN SHEARED G(DOT)A AND A(DOT)G BASE-PAIRS TO FORM AN INTERESTING NEW STRUCTURAL MOTIF, THE GA-BRACKETED G-STACK. THE TGGAA REPEAT UNIT CONTAINS SIX "STEPS", FOUR OF WHICH ARE NOT WATSON-CRICK BASE-PAIRS.
NMR ensembleConformers submitted total number: 1

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