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- PDB-327d: CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC) -

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Basic information

Entry
Database: PDB / ID: 327d
TitleCRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)
ComponentsDNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*CP*GP*CP*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.94 Å
AuthorsTippin, D.B. / Ramakrishnan, B. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Methylation of the Z-DNA decamer d(GC)5 potentiates the formation of A-DNA: crystal structure of d(Gm5CGm5CGCGCGC).
Authors: Tippin, D.B. / Ramakrishnan, B. / Sundaralingam, M.
History
DepositionMar 17, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0May 22, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,0751
Polymers3,0751
Non-polymers00
Water73941
1
A: DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*CP*GP*CP*GP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)6,1502
Polymers6,1502
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)39.330, 39.330, 77.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-42-

HOH

21A-44-

HOH

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Components

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


Mass: 3075.035 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
162 mMsodium cacodylate1drop
21 mMDNA1dropsingle strand
32 mMspermine tetrachloride1drop
412 mMammonium acetate1drop
575 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.94 Å / Num. obs: 2601 / % possible obs: 86.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052
Reflection
*PLUS
Highest resolution: 1.94 Å / % possible obs: 86.8 % / Num. measured all: 12315

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Processing

Software
NameClassification
X-PLORrefinement
MSCdata reduction
RefinementResolution: 1.94→8 Å / σ(F): 1
RfactorNum. reflection
Rfree0.227 -
Rwork0.191 -
obs0.191 2533
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.94→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 2 41 245
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.08
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 8 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS

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