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- PDB-115d: ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESO... -

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Basic information

Entry
Database: PDB / ID: 115d
TitleORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESOLUTION
ComponentsDNA (5'-D(*GP*GP*(BRU)P*AP*(BRU)P*AP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsKennard, O. / Cruse, W.B.T. / Nachman, J. / Prange, T. / Shakked, Z. / Rabinovich, D.
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 1986
Title: Ordered water structure in an A-DNA octamer at 1.7 A resolution.
Authors: Kennard, O. / Cruse, W.B. / Nachman, J. / Prange, T. / Shakked, Z. / Rabinovich, D.
#1: Journal: Nature / Year: 1989
Title: Coexistence of A-and B-Form DNA in a Single Crystal Lattice
Authors: Doucet, J. / Benoit, J.-P. / Cruse, W.B.T. / Prange, T. / Kennard, O.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Sequence-Dependent Conformation of an A-DNA Double Helix. The Crystal Structure of the Octamer d(G-G-T-A-T-A-C-C)
Authors: Shakked, Z. / Rabinovich, D. / Kennard, O. / Cruse, W.B.T. / Salisbury, S.A. / Viswamitra, M.A.
#3: Journal: Proc.R.Soc.London,Ser.B / Year: 1981
Title: Crystalline A-DNA. The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C)
Authors: Shakked, Z. / Rabinovich, D. / Cruse, W.B.T. / Egert, E. / Kennard, O. / Sala, G. / Salisbury, S.A. / Viswamitra, M.A.
History
DepositionFeb 12, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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*(BRU)P*AP*(BRU)P*AP*CP*C)-3')
B: DNA (5'-D(*GP*GP*(BRU)P*AP*(BRU)P*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1132
Polymers5,1132
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.084, 45.084, 41.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: DNA chain DNA (5'-D(*GP*GP*(BRU)P*AP*(BRU)P*AP*CP*C)-3')


Mass: 2556.357 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %MPD1drop
20.4 mMoligonucleotide1reservoir
30.28 mMMg acetate1reservoir
40.4 mMspermine hydrochloride1reservoir
515 %MPD1reservoir
61

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Data collection

Diffraction
IDAmbient temp detailsCrystal-ID
1ROOM TEMPERATURE1
21
Diffraction source
SourceSiteTypeID
SEALED TUBE1
SYNCHROTRONLURE LURE 2
Detector
TypeIDDetector
ENRAF-NONIUS CAD41DIFFRACTOMETER
PHILLIPS2OSCILLATION CAMERA
Radiation
IDMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mx-ray1
2Mx-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionHighest resolution: 1.7 Å / Num. obs: 4669 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. all: 5833 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.097

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.7→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.14 4428
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 318 4 85 407
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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