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- PDB-1o56: MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC AC... -

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Basic information

Entry
Database: PDB / ID: 1o56
TitleMOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION
ComponentsDNA (5'-CD(*AP*AP*AP*)-3')
KeywordsDNA / CYCLIC TRINUCLEOTIDE
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 0.9 Å
AuthorsGao, Y.G. / Robinson, H. / Guan, Y. / Liaw, Y.C. / van Boom, J.H. / van der Marel, G.A. / Wang, A.H.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1998
Title: Molecular structure of two crystal forms of cyclic triadenylic acid at 1A resolution.
Authors: Gao, Y.G. / Robinson, H. / Guan, Y. / Liaw, Y.C. / van Boom, J.H. / van der Marel, G.A. / Wang, A.H.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionAug 26, 2003ID: 416d
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The crystallized entity is 5'-CD(*AP*AP*AP)-3', however, each of the two independent ...SEQUENCE The crystallized entity is 5'-CD(*AP*AP*AP)-3', however, each of the two independent molecules sits on the crystallographic 3-fold axis. Remark 350 provides the way to create cyclic D(*Ap*Ap*Ap) molecule.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-CD(*AP*AP*AP*)-3')
B: DNA (5'-CD(*AP*AP*AP*)-3')


Theoretical massNumber of molelcules
Total (without water)1,7892
Polymers1,7892
Non-polymers00
Water23413
1
A: DNA (5'-CD(*AP*AP*AP*)-3')

A: DNA (5'-CD(*AP*AP*AP*)-3')

A: DNA (5'-CD(*AP*AP*AP*)-3')


Theoretical massNumber of molelcules
Total (without water)2,6843
Polymers2,6843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
B: DNA (5'-CD(*AP*AP*AP*)-3')

B: DNA (5'-CD(*AP*AP*AP*)-3')

B: DNA (5'-CD(*AP*AP*AP*)-3')


  • defined by author
  • 2.68 kDa, 3 polymers
Theoretical massNumber of molelcules
Total (without water)2,6843
Polymers2,6843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)23.328, 23.328, 9.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-4-

HOH

21A-5-

HOH

31A-6-

HOH

41A-12-

HOH

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Components

#1: DNA chain DNA (5'-CD(*AP*AP*AP*)-3')


Mass: 894.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.41 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2GLYCINE11
3MGCL211
4MPD12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 29, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 0.9→10 Å / Num. obs: 3059 / Observed criterion σ(F): 3

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
RefinementResolution: 0.9→10 Å / σ(F): 3 /
RfactorNum. reflection
all0.109 3059
obs-3059
Refinement stepCycle: LAST / Resolution: 0.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 42 0 13 55
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.032
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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