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- PDB-187d: HYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYST... -

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Basic information

Entry
Database: PDB / ID: 187d
TitleHYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYSTAL STRUCTURES. IMPLICATIONS FOR DNA RECOGNITION
ComponentsDNA (5'-D(*CP*CP*CP*CP*GP*GP*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsEisenstein, M. / Shakked, Z.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition.
Authors: Eisenstein, M. / Shakked, Z.
#1: Journal: J.Biomol.Struct.Dyn. / Year: 1987
Title: The Crystal Structure of d(CCCCGGGG): A New A-Form Variant with an Extended Backbone Conformation
Authors: Haran, T.E. / Shakked, Z. / Wang, A.H.-J. / Rich, A.
History
DepositionSep 2, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,4291
Polymers2,4291
Non-polymers00
Water70339
1
A: DNA (5'-D(*CP*CP*CP*CP*GP*GP*GP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)43.360, 43.360, 24.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-20-

HOH

21A-47-

HOH

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Components

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


Mass: 2428.593 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4SPERMINE11
5MGCL211
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7 / Method: unknown
Details: Wang, A. H.-J., (1982) Proc. Nat. Acad. Sci. USA., 79, 3968.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
125 mMsodium cacodylate1
20.6 mMspermine1
33 mM1MgCl2
41.2 mMoctamer1
530 %MPD12
61
71

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Data collection

DiffractionMean temperature: 288 K
DetectorType: NICOLET / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.25 Å
Reflection
*PLUS
Highest resolution: 2.25 Å

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.25→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.134 816
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 39 200
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.0060.02
X-RAY DIFFRACTIONn_angle_d0.0190.04
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it1.4383
X-RAY DIFFRACTIONn_sugar_angle_it2.255
X-RAY DIFFRACTIONn_phos_bond_it1.2923
X-RAY DIFFRACTIONn_phos_angle_it2.3175
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d0.0130.03
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0340.06
X-RAY DIFFRACTIONn_plane_restr0.0070.02
X-RAY DIFFRACTIONn_chiral_restr0.010.04
X-RAY DIFFRACTIONn_singtor_nbd0.1290.2
X-RAY DIFFRACTIONn_multtor_nbd0.160.2
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.134
Solvent computation
*PLUS
Displacement parameters
*PLUS

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