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- PDB-118d: CRYSTAL AND MOLECULAR STRUCTURE OF D(GTGCGCAC): INVESTIGATION OF ... -

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Basic information

Entry
Database: PDB / ID: 118d
TitleCRYSTAL AND MOLECULAR STRUCTURE OF D(GTGCGCAC): INVESTIGATION OF THE EFFECTS OF BASE SEQUENCE ON THE CONFORMATION OF OCTAMER DUPLEXES
ComponentsDNA (5'-D(*GP*TP*GP*CP*GP*CP*AP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.64 Å
AuthorsBingman, C.A. / Li, X. / Zon, G. / Sundaralingam, M.
CitationJournal: Biochemistry / Year: 1992
Title: Crystal and molecular structure of d(GTGCGCAC): investigation of the effects of base sequence on the conformation of octamer duplexes.
Authors: Bingman, C.A. / Li, X. / Zon, G. / Sundaralingam, M.
History
DepositionFeb 11, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 11, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 22, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _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*GP*CP*GP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4281
Polymers2,4281
Non-polymers00
Water75742
1
A: DNA (5'-D(*GP*TP*GP*CP*GP*CP*AP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.220, 42.220, 25.070
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-50-

HOH

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Components

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


Mass: 2427.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 46.55 %
Crystal growMethod: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MGCL211
3SPERMINE11
4NA CACODYLATE11
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMoctamer duplex1drop
23 mM1dropMgCl2
32 mMspermine1drop
410 mMsodium cacodylate1drop
53.0 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.64 Å / Num. all: 11665 / Num. obs: 2767 / Observed criterion σ(I): 4
Reflection
*PLUS
% possible obs: 91.6 % / Num. measured all: 11665 / Rmerge(I) obs: 0.035

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.64→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.154 4483
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.64→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 42 203
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.0050.025
X-RAY DIFFRACTIONn_angle_d0.0170.05
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
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_restr0.0150.04
X-RAY DIFFRACTIONn_chiral_restr0.0530.1
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd0.1420.09
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.64 Å / Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.0050.025
X-RAY DIFFRACTIONn_angle_d0.0170.05

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