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- PDB-141d: SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GEN... -

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Basic information

Entry
Database: PDB / ID: 141d
TitleSOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH DISTANCE AND TORSION ANGLE RESTRAINTS DERIVED FROM TWO-DIMENSIONAL NMR SPECTRA
Components
  • DNA (5'-D(*AP*GP*CP*TP*TP*GP*CP*CP*TP*TP*GP*AP*G)-3')
  • DNA (5'-D(*CP*TP*CP*AP*AP*GP*GP*CP*AP*AP*GP*CP*T)-3')
KeywordsDNA / DOUBLE HELIX / CONSERVED SEQUENCE OF HIV-1 GENOME
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, ENERGY MINIMIZATION
AuthorsMujeeb, A. / James, T.L.
CitationJournal: Biochemistry / Year: 1993
Title: Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra.
Authors: Mujeeb, A. / Kerwin, S.M. / Kenyon, G.L. / James, T.L.
History
DepositionSep 24, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: 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: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*CP*TP*TP*GP*CP*CP*TP*TP*GP*AP*G)-3')
B: DNA (5'-D(*CP*TP*CP*AP*AP*GP*GP*CP*AP*AP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,9432
Polymers7,9432
Non-polymers00
Water0
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(*AP*GP*CP*TP*TP*GP*CP*CP*TP*TP*GP*AP*G)-3')


Mass: 3982.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#2: DNA chain DNA (5'-D(*CP*TP*CP*AP*AP*GP*GP*CP*AP*AP*GP*CP*T)-3')


Mass: 3960.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: SUGAR PUCKER OF DEOXYRIBOSES HAS BEEN DETERMINED BY SIMULATION OF 2QF-COSY SPECTRA. A LIST OF TORSION ANGLE AND NOE DISTANCE RESTRAINTS IS AVAILABLE FROM THE PROTEIN DATA BANK AS ENTRY R140DMR.

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameClassification
AMBER4structure solution
AMBER4refinement
RefinementMethod: MOLECULAR DYNAMICS, ENERGY MINIMIZATION / Software ordinal: 1
Details: ALL COORDINATES AROSE FROM ENERGY MINIMIZED AMBER4 FILES THAT WERE REFORMATTED FOR THE HELIX ANALYSIS PROGRAM CURVES. THEREFORE, ALL HYDROGEN ATOMS WERE REMOVED. THE DEPOSITORS HAVE PROVIDED ...Details: ALL COORDINATES AROSE FROM ENERGY MINIMIZED AMBER4 FILES THAT WERE REFORMATTED FOR THE HELIX ANALYSIS PROGRAM CURVES. THEREFORE, ALL HYDROGEN ATOMS WERE REMOVED. THE DEPOSITORS HAVE PROVIDED THREE COORDINATE SETS FOR THIS STRUCTURE. THE FIRST TWO COORDINATE SETS (PROTEIN DATA BANK ENTRIES 140D AND 141D) CONTAIN THE RESULTS OF THE NMR/RESTRAINED MOLECULAR DYNAMICS REFINEMENT WHERE A-DNA AND B-DNA WERE USED AS STARTING MODELS, RESPECTIVELY. THE AUTHORS DENOTED THESE STRUCTURES AS RMD-A AND RMD-B, RESPECTIVELY. THE THIRD COORDINATE SET (PROTEIN DATA BANK ENTRY 142D) REPRESENTS THE FINAL STRUCTURE, DENOTED RMD-FINAL BY THE AUTHORS. ALL STRUCTURES WERE DERIVED BY AVERAGING THE LAST 4 PS OF 30 PS RESTRAINED MD (AMBER4) AND SUBSEQUENT RESTRAINED ENERGY MINIMIZATION. FIVE RMD RUNS WERE AVERAGED TO EACH INTERIM STRUCTURE RMD-A AND RMD-B, DEPENDING ON THE STARTING GEOMETRY. ALL TEN STRUCTURES WERE AVERAGED, RESTRAINED ENERGY MINIMIZED AND A FINAL 20PS RMD RUN WAS PERFORMED, THE LAST 4PS OF WHICH, AFTER AVERAGING AND RESTRAINED ENERGY MINIMIZATION LEAD TO THE FINAL STRUCTURE: RMD-FINAL.
NMR ensembleConformers submitted total number: 1

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