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- PDB-138d: A-DNA DECAMER D(GCGGGCCCGC)-HEXAGONAL CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 138d
TitleA-DNA DECAMER D(GCGGGCCCGC)-HEXAGONAL CRYSTAL FORM
ComponentsDNA (5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsRamakrishnan, B. / Sundaralingam, M.
CitationJournal: Biochemistry / Year: 1993
Title: Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and ...Title: Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and comparison with their isomorphous crystal structures.
Authors: Ramakrishnan, B. / Sundaralingam, M.
History
DepositionSep 15, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 15, 1994Provider: 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*CP*GP*GP*GP*CP*CP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,0471
Polymers3,0471
Non-polymers00
Water68538
1
A: DNA (5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)6,0942
Polymers6,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)39.110, 39.110, 79.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 3046.980 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3[CO(NH3)6]CL311
4WATER12
5MPD12

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 3435
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / % possible obs: 91 % / Num. measured all: 19222 / Rmerge(I) obs: 0.039

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.183 -
obs0.183 2298
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 0 38 240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d31.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.9
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 2298 / σ(F): 3 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg3.9

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