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- PDB-272d: PARALLEL AND ANTIPARALLEL (G.GC)2 TRIPLE HELIX FRAGMENTS IN A CRY... -

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Basic information

Entry
Database: PDB / ID: 272d
TitlePARALLEL AND ANTIPARALLEL (G.GC)2 TRIPLE HELIX FRAGMENTS IN A CRYSTAL STRUCTURE
ComponentsDNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / INTERMOLECULAR BASE TRIPLET / OVERHANGING BASES
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVlieghe, D. / Van Meervelt, L. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O.
CitationJournal: Science / Year: 1996
Title: Parallel and antiparallel (G.GC)2 triple helix fragments in a crystal structure.
Authors: Vlieghe, D. / Van Meervelt, L. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O.
History
DepositionJul 9, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 20, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). TWO TYPES OF TRIPLEXES CAN BE GENERATED - PARALLEL TRIPLEX AND ANTIPARALLEL TRIPLEX. ONLY THE SYMMETRY OPERATIONS WHICH GENERATE THE PARALLEL TRIPLEX ARE SHOWN IN REMARK 350. THE PARALLEL TRIPLEX IS GENERATED BY APPLYING SYMMETRY OPERATION 1/2-X, 1-Y, 1/2+Z. THE ANTIPARALLEL TRIPLEX IS GENERATED BY APPLYING SYMMETRY OPERATION 1-X, 1/2+Y, 1/2-Z.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,1702
Polymers6,1702
Non-polymers00
Water79344
1
A: DNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
B: DNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')

A: DNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
B: DNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,3404
Polymers12,3404
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Unit cell
Length a, b, c (Å)26.250, 36.820, 53.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3085.029 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 289.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.4 mMDNA1drop
243 mM1dropMgCl2
30.6 mMspermine1drop
43 %MPD1drop
540 %MPD1reservoir
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→14.5 Å / Num. all: 12303 / Num. obs: 3534 / % possible obs: 94.6 % / Redundancy: 3 % / Rsym value: 0.046 / Net I/σ(I): 5.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.193 / % possible all: 86.3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 14.5 Å / % possible obs: 94.6 % / Redundancy: 3 % / Num. measured all: 12303 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 86.3 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
AMoRE(J. NAVAZA)phasing
SHELXL-93refinement
IPMOSFLMdata reduction
ABSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / Num. parameters: 1818 / Num. restraintsaints: 1990 / σ(F): 0 /
RfactorNum. reflection
obs0.209 3514
all-3514
Solvent computationSolvent model: BABINET'S PRINCIPLE
Displacement parametersBiso mean: 30.6 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 410 0 44 454
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 3212 / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.6 Å2

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