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- PDB-441d: HIGH RESOLUTION A-DNA CRYSTAL STRYCTURES OF D(AGGGGCCCCT): AN A-D... -

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Basic information

Entry
Database: PDB / ID: 441d
TitleHIGH RESOLUTION A-DNA CRYSTAL STRYCTURES OF D(AGGGGCCCCT): AN A-DNA MODEL OF POLY(DG).POLY(DC)
ComponentsDNA (5'-D(*AP*GP*GP*GP*GP*CP*CP*CP*CP*T)-3')
KeywordsDNA / HIGH RESOLUTION / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsGao, Y.G. / Robinson, H.H. / Wang, A.H.
CitationJournal: Eur.J.Biochem. / Year: 1999
Title: High-resolution A-DNA crystal structures of d(AGGGGCCCCT). An A-DNA model of poly(dG) x poly(dC).
Authors: Gao, Y.G. / Robinson, H. / Wang, A.H.
History
DepositionJan 13, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Jan 15, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 19, 2014Group: Other
Revision 1.4May 3, 2017Group: Source and taxonomy / Structure summary
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,0461
Polymers3,0461
Non-polymers00
Water1,40578
1
A: DNA (5'-D(*AP*GP*GP*GP*GP*CP*CP*CP*CP*T)-3')

A: DNA (5'-D(*AP*GP*GP*GP*GP*CP*CP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)32.765, 32.765, 77.754
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122

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Components

#1: DNA chain DNA (5'-D(*AP*GP*GP*GP*GP*CP*CP*CP*CP*T)-3')


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.947 Å3/Da / Density % sol: 37.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MPD11
3MGCL211
4MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.63 mMDNA duplex1
250 mMsodium cacodylate1
37.5 %MPD1
440 %1
525 mM11can be replaced by 10mM [Co(NH3)6]3+Mg2+

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.540598
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 15, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540598 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. obs: 4385 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 1.49→1.56 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.334 / % possible all: 96.5
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
bioteXdata reduction
bioteXdata scaling
X-PLORphasing
RefinementResolution: 1.5→6 Å / Cross valid method: THROUGHOUT / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.315 277 10 %RANDOM
Rwork0.236 ---
all0.239 ---
obs0.236 2775 61.6 %-
Refinement stepCycle: LAST / Resolution: 1.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 0 78 280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.22
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 4 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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