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- PDB-1d82: CRYSTAL AND MOLECULAR STRUCTURE OF D(GTCTAGAC) -

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Basic information

Entry
Database: PDB / ID: 1d82
TitleCRYSTAL AND MOLECULAR STRUCTURE OF D(GTCTAGAC)
ComponentsDNA (5'-D(*GP*TP*CP*TP*AP*GP*AP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsCervi, A. / Langlois D'Estaintot, B. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Crystal and Molecular Structure of d(GTCTAGAC)
Authors: Cervi, A. / Langlois D'Estaintot, B. / Hunter, W.N.
History
DepositionJun 29, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 15, 1992Provider: 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(*GP*TP*CP*TP*AP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4271
Polymers2,4271
Non-polymers00
Water543
1
A: DNA (5'-D(*GP*TP*CP*TP*AP*GP*AP*C)-3')

A: DNA (5'-D(*GP*TP*CP*TP*AP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8532
Polymers4,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.560, 42.560, 24.610
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*TP*CP*TP*AP*GP*AP*C)-3')


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.8 / Details: pH 6.80, VAPOR DIFFUSION, temperature 295.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 295 K / pH: 6.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlDNA1drop
260 mMsodium cacodylate1drop
325 mMmagnesium cacodylate1drop
46 mMspermine tetrachloride1drop
510 %(v/v)MPD1drop
650 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 1861 / Num. obs: 1757 / Observed criterion σ(F): 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Observed criterion σ(F): 1

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→6 Å / σ(F): 1 /
RfactorNum. reflection
obs0.211 801
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 3 164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it0.011
X-RAY DIFFRACTIONn_sugar_angle_it0.023
X-RAY DIFFRACTIONn_phos_bond_it0.031
X-RAY DIFFRACTIONn_phos_angle_it0.044
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_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS

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