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- PDB-3g2a: Crystal structure of d(CACGCG).d(CGCGTG) grown in presence of 1mM... -

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Basic information

Entry
Database: PDB / ID: 3g2a
TitleCrystal structure of d(CACGCG).d(CGCGTG) grown in presence of 1mM MnCl2
Components
  • 5'-D(*CP*AP*CP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*GP*TP*G)-3'
KeywordsDNA / double helical Z form DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Kannan, R. / Gautham, N.
CitationJournal: To be Published
Title: Crystal Structures of d(CACGCG).d(CGCGTG) cocrystallized with MnCl2
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionJan 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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: 5'-D(*CP*AP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)3,6192
Polymers3,6192
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-6 kcal/mol
Surface area2340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.835, 30.907, 44.731
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 5'-D(*CP*AP*CP*GP*CP*G)-3'


Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*CP*GP*TP*G)-3'


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.7 Å3/Da / Density % sol: 27.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.99
Details: 50mM Sodium Cacodylate, 1mM MnCl2, 1mM Spermine, 50% Methyl pentane diol, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium cacoldylate11
2MnCl211
3Spermine11
4MPD11
5Sodium cacoldylate12
6MnCl212
7MPD12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 2008
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 1914 / Num. obs: 1819 / % possible obs: 95.2 % / Redundancy: 4.56 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.0896 / Net I/σ(I): 4.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.69 % / Rmerge(I) obs: 0.2886 / Mean I/σ(I) obs: 1.2 / Num. unique all: 172 / Rsym value: 0.258 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.965 / SU B: 5.557 / SU ML: 0.146 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24078 77 4.3 %RANDOM
Rwork0.23882 ---
obs0.23892 1711 96.08 %-
all-1711 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.664 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 24 264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021268
X-RAY DIFFRACTIONr_angle_refined_deg3.7673410
X-RAY DIFFRACTIONr_chiral_restr0.1770.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02126
X-RAY DIFFRACTIONr_nbd_refined0.1820.284
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.27
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.24
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.105 4 -
Rwork0.329 123 -
obs-123 99.22 %

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