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- PDB-189d: HYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYST... -

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Entry
Database: PDB / ID: 189d
TitleHYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYSTAL STRUCTURES. IMPLICATIONS FOR DNA RECOGNITION
ComponentsDNA (5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
MethodX-RAY DIFFRACTION / Resolution: 2.1 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: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Molecular Structure of the Octamer d(G-G-C-C-G-G-C-C): Modified A-DNA
Authors: Wang, A.H.-J. / Fujii, S. / Boom, J.H.V. / Rich, A.
Validation Report
SummaryFull reportAbout validation report
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,4291
Polymers2,4291
Non-polymers00
Water72140
1
A: DNA (5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-3')

A: DNA (5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-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
γ
α
β
Length a, b, c (Å)42.040, 42.040, 25.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(*GP*GP*CP*CP*GP*GP*CP*C)-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.: 40 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Components of the solutions

Crystal-ID: 1

IDNameSol-ID
1WATER1
2MPD1
3NA CACODYLATE1
4SPERMINE1
5MGCL21
6WATER2
7MPD2
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

Crystal-ID: 1

IDConc.Common nameChemical formulaSol-ID
125 mMsodium cacodylate
20.6 mMspermine
33 mMMgCl2
41.2 mMoctamer
530 %MPD2
6
7

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Data collection

DiffractionMean temperature: 288 K
DetectorType: NICOLET / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.1→8 Å / σ(F): 2 /
RfactorNum. reflection
Obs0.152 1388
Refine Biso

Refinement-ID: X-RAY DIFFRACTION / Details: TR / Treatment: isotropic

Class
ALL ATOMS
ALL WATERS
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 40 201
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
n_bond_d0.0070.02
n_angle_d0.0210.04
n_planar_d
n_hb_or_metal_coord
n_sugar_bond_it1.6833
n_sugar_angle_it2.5425
n_phos_bond_it2.1343
n_phos_angle_it2.7455
n_bond_angle_restr
n_dihedral_angle_restr
n_impr_tor
n_sugar_bond_d
n_sugar_bond_angle_d
n_phos_bond_d0.0180.03
n_phos_bond_angle_d0.050.06
n_plane_restr0.0070.02
n_chiral_restr0.0090.03
n_singtor_nbd0.0840.2
n_multtor_nbd0.1380.2
n_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.152

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