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- PDB-213d: CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCIGGCCM5CGG) AT 1.6 ANG... -

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Basic information

Entry
Database: PDB / ID: 213d
TitleCRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCIGGCCM5CGG) AT 1.6 ANGSTROMS SHOWING THE UNEXPECTED WOBBLE I.M5C BASE PAIR
ComponentsDNA (5'-D(*CP*CP*IP*GP*GP*CP*CP*(5CM)P*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsRamakrishnan, B. / Sundaralingam, M.
CitationJournal: Biophys.J. / Year: 1995
Title: Crystal structure of the A-DNA decamer d(CCIGGCCm5CGG) at 1.6 A showing the unexpected wobble I.m5C base pair.
Authors: Ramakrishnan, B. / Sundaralingam, M.
History
DepositionJun 28, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 31, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*IP*GP*GP*CP*CP*(5CM)P*GP*G)-3')
B: DNA (5'-D(*CP*CP*IP*GP*GP*CP*CP*(5CM)P*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.020, 44.950, 47.620
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(*CP*CP*IP*GP*GP*CP*CP*(5CM)P*GP*G)-3')


Mass: 3045.993 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 44.03 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mMDNA1drop
240 mMsodium cacodylate1drop
35 mMspermine tetrachloride1drop
450 %(v/v)MPD1reservoir
51
61

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. all: 21000 / Num. obs: 6143
Reflection
*PLUS
Highest resolution: 1.6 Å / % possible obs: 86 % / Num. measured all: 21000 / Rmerge(I) obs: 0.021

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.6→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.163 -
obs0.163 5119
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 402 2 103 507
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_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 1.6 Å / Lowest resolution: 8 Å / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg31.9
X-RAY DIFFRACTIONx_improper_angle_deg3.1

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