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- PDB-137d: A-DNA DECAMER D(GCGGGCCCGC)-ORTHORHOMBIC CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 137d
TitleA-DNA DECAMER D(GCGGGCCCGC)-ORTHORHOMBIC 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: 1.7 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')
B: 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
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.900, 44.840, 47.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
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
3SPERMINE_HCL11
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: 1.7→8 Å / Num. obs: 6219
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / % possible obs: 97 % / Num. measured all: 17581 / Rmerge(I) obs: 0.028

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.7→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.185 -
obs0.185 5450
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 101 505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_d3.1
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: 1.7 Å / Lowest resolution: 8 Å / Num. reflection obs: 5450 / σ(F): 3 / Rfactor obs: 0.185
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_deg3.1

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