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- PDB-1gip: THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS DILUTE L... -

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Entry
Database: PDB / ID: 1gip
TitleTHE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS DILUTE LIQUID CRYSTALLINE PHASE
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / B-DNA / DIPOLAR COUPLING / NOE / BASE-BASE ORIENTATIONAL POTENTIAL OF MEAN FORCE / DATABASE TORSION ANGLE POTENTIAL OF MEAN FORCE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING IN TORSION ANGLE SPACE USING A SIXTH ORDER PREDICTOR-CORRECTOR METHOD WITH AUTOMATIC TIME STEP SELECTION (C. SCHWIETERS, G.M. CLORE)
AuthorsClore, G.M. / Kuszewski, J.
Citation
Journal: J.Am.Chem.Soc. / Year: 2001
Title: Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.
Authors: Kuszewski, J. / Schwieters, C. / Clore, G.M.
#1: Journal: J.Am.Chem.Soc. / Year: 2000
Title: The NMR Structure of a DNA Dodecamer in an Aqueous Dilute Liquid Crystalline Phase
Authors: Tjandra, N. / Tate, S. / Ono, A. / Kainosho, M. / Bax, A.
History
DepositionFeb 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: 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: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
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)2 / 40THE RESTRAINED REGULARIZED MEAN STRUCTURES
Representative

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-HSQC-J-MODULATED
121COSY
13113C-HSQC-F1- COUPLED
14115N-HSQC-F1- COUPLED
1512D NOESY
NMR detailsText: THE NUMBER OF CALCULATED CONFORMERS IS 20 WITH NOES AND DIPOLAR COUPLINGS AND 20 WITH DIPOLAR COUPLINGS ONLY

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Sample preparation

DetailsContents: 0.5 MM DUPLEX DNA, 40MM SODIUM PHOSPHATE, PH 7.0
Sample conditionsIonic strength: 40 mM / pH: 7 / Pressure: 1 atm / Temperature: 308.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
NIH VERSION OF XPLOR (AVAILABLE TO ACADEMIC USERS BY ANONYMOUS FTP AT PORTAL.NIDDK.NIH.GOV IN pub/clore/xplor_nih)CLORE, SCHWIETERS AND KUSZEWSKI. ADAPTED FROM XPLOR 3.841 by BRUNGER ET AL.refinement
NMRPIPE 1.71999.039.11.31structure solution
XwinNMR2.4structure solution
PIPP/CAPP4.2.8structure solution
RefinementMethod: SIMULATED ANNEALING IN TORSION ANGLE SPACE USING A SIXTH ORDER PREDICTOR-CORRECTOR METHOD WITH AUTOMATIC TIME STEP SELECTION (C. SCHWIETERS, G.M. CLORE)
Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 48 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 137 DIHEDRAL 137 TORSION ANGLE RESTRAINTS, 198 CH AND 10 NH ONE-BOND DIPOLAR COUPLING ...Details: THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 48 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, AND 137 DIHEDRAL 137 TORSION ANGLE RESTRAINTS, 198 CH AND 10 NH ONE-BOND DIPOLAR COUPLING RESTRAINTS, AND 200 APPROXIMATE PROTON-PROTON DIPOLAR COUPLINGS. THE EXPERIMENTAL RESTRAINTS ARE THE SAME AS THOSE LISTED IN 1DUF. THE NON-BONDED CONTACTS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM AND A BASE-BASE POSITIONING DATABASE POTENTIAL OF MEAN FORCE. ALSO INCLUDED IS A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE. IN THIS ENTRY THE SECOND TO LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. MODEL 1 IS CALCULATED WITH NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, DIPOLAR COUPLING RESTRAINTS AND TORSION ANGLE RESTRAINTS. MODEL 2 IS CALCULATED WITH DIPOLAR COUPLING AND TORSION ANGLE RESTRAINTS. NO NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS WERE EMPLOYED. STRUCTURAL STATISTICS: ---------------------------------------------------------- RESTRAINTS MODEL 1 MODEL 2 (# MODEL 1/# MODEL 2) (NOE + DIPOLARS) (DIPOLARS ONLY) ---------------------------------------------------------- RMS DEVIATIONS FROM EXPERIMENTAL RESTRAINTS INTERPROTON DISTANCES (A) 0.065 0.114 (162/0) TORSION ANGLES (DEG) 0 0 (137/137) ALL DIPOLAR COUPLINGS (HZ) 2.8 2.6 (408/408) RMS DEVIATIONS AND DIPOLAR COUPLING R-FACTORS FOR DIFFERENT CLASSES OF DIPOLAR COUPLINGS C-H RIBOSE (HZ/%) (94/94)* 2.27 (11.4%) 2.27 (11.4%) C-H RIBOSE (HZ/%) (64/64)** 5.62 (28.1%) 5.24 (26.2%) C-H BASE (HZ/%) (24/24)* 2.78 (13.9%) 2.81 (14.1%) C-H BASE (HZ/%) (12/12)** 1.89 (9.26%) 2.01 (10.0%) C-H METHYL (HZ/%) (4/4)* 0.98 (4.9%) 0.79 (4.0%) N-H IMINO (HZ/%) (10/10)* 1.56 (15.9%) 1.50 (15.2%) H-H ABSOLUTE VALUE (HZ) (126/126) 1.26 1.25 H-H SIGN KNOWN (HZ) (74/74) 0.93 0.88 RMS DEVIATIONS FROM IDEALIZED COVALENT GEOMETRY BONDS (A) 0.003 0.003 ANGLES (DEG) 0.897 0.925 IMPROPER TORSIONS (DEG) 0.296 0.106 ---------------------------------------------------------- * MEASURED WITH AN ACCURACY OF +/- 2 HZ ** MEASURED WITH AN ACCURACY OF +/- 4 HZ DIPOLAR COUPLING R-FACTOR = RATIO RMS DEVIATION BETWEEN OBSERVED AND CALCULATED VALUES AND EXPECTED RMS DEVIATION IF VECTORS ARE RANDOMLY DISTRIBUTED. THE LATTER IS GIVEN BY {2DA**2[4 + 3H**2]/5}1/2 WHERE DA IS THE MAGNITUDE OF THE AXIAL COMPONENT OF THE ALIGNMENT TENSOR AND H IS THE RHOMBICITY. (ONLY APPLIES TO FIXED LENGTH VECTORS). THE VALUES OF DA(CH), DA(NH) AND H ARE -16 HZ, -7.7 HZ AND 0.26, RESPECTIVELY.
NMR ensembleConformer selection criteria: THE RESTRAINED REGULARIZED MEAN STRUCTURES
Conformers calculated total number: 40 / Conformers submitted total number: 2

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