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- PDB-440d: HIGH RESOLUTION A-DNA CRYSTAL STRYCTURES OF D(AGGGGCCCCT): AN A-D... -

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Basic information

Entry
Database: PDB / ID: 440d
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 / DUPLEX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.1 Å
AuthorsGao, Y.-G. / Robinson, H.H. / Wang, A.H.-J.
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 1.4Feb 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')
B: 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
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.688, 45.004, 46.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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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.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.099 Å3/Da / Density % sol: 42.32 %
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
3SPERMINE11
4MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.63 mMDNA duplex1
250 mMsodium cacodylate1
37.5 %MPD1
440 %1
51.3 mMspermine11

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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: Nov 11, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540598 Å / Relative weight: 1
ReflectionResolution: 1.1→10 Å / Num. obs: 17722 / % possible obs: 80.5 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.0509 / Net I/σ(I): 14.3
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.1 / % possible all: 57

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
bioteXdata reduction
bioteXdata scaling
X-PLORphasing
RefinementResolution: 1.1→10 Å / Num. parameters: 4183 / Num. restraintsaints: 5156 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 879 5 %RANDOM
Rwork0.213 ---
obs0.214 17587 79.9 %-
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 135 539
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.053
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.1 Å / Num. reflection obs: 13095 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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