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- PDB-1r3z: Crystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effect... -

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Basic information

Entry
Database: PDB / ID: 1r3z
TitleCrystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effects of methylation on alternating DNA octamers
Components5'-D(*GP*(5CM)P*GP*(5CM)P*GP*CP*GP*C)-3'
KeywordsDNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Molecular Placement / Resolution: 1.7 Å
AuthorsShi, K. / Pan, B. / Tippin, D. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.
Authors: Shi, K. / Pan, B. / Tippin, D. / Sundaralingam, M.
History
DepositionOct 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,4571
Polymers2,4571
Non-polymers00
Water45025
1
A: 5'-D(*GP*(5CM)P*GP*(5CM)P*GP*CP*GP*C)-3'

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


Theoretical massNumber of molelcules
Total (without water)4,9132
Polymers4,9132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.97, 42.97, 24.93
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 2456.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Synthesizer
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: cacodylate, magnesium chloride, spermine tetrachloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2magnesium chloride11
3spermine tetrachloride11
4H2O11
5cacodylate12
6magnesium chloride12
7spermine tetrachloride12
8H2O12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMDNA1drop
225 mMsodium cacodylate1droppH6.0
31 mM1dropMgCl2
40.5 mMspermine tetrachloride1drop
540 %MPD1reservoir
61
71
81

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→10 Å / Num. all: 2799 / Num. obs: 2540 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.7 Å / % possible all: 90.7
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 2711 / % possible obs: 90 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 80.5 % / Rmerge(I) obs: 0.2

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: Molecular Placement / Resolution: 1.7→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.203 229 RANDOM
Rwork0.17 --
all0.193 2540 -
obs0.193 2311 -
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 163 0 25 188
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.02
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.313 / Rfactor Rwork: 0.262

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