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- PDB-3g2r: Crystal structure of d(CACGCG).d(CGCGTG) cocrystallized with MnCl2 -

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Basic information

Entry
Database: PDB / ID: 3g2r
TitleCrystal structure of d(CACGCG).d(CGCGTG) cocrystallized with MnCl2
Components5'-D(*CP*GP*TP*GP*CP*G)-3'
KeywordsDNA / duplex Z-form DNA with Watson-Crick base pairing
Function / homology2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / : / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Kannan, R. / Gautham, N.
CitationJournal: To be Published
Title: Crystal studies of d(CACGCG).d(CGCGTG) grown with various counter ions
Authors: Venkadesh, S. / Mandal, P.K. / Kannan, R. / Gautham, N.
History
DepositionFeb 1, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*GP*TP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,1873
Polymers1,8251
Non-polymers3622
Water1086
1
A: 5'-D(*CP*GP*TP*GP*CP*G)-3'
hetero molecules

A: 5'-D(*CP*GP*TP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3756
Polymers3,6502
Non-polymers7244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area480 Å2
ΔGint-9 kcal/mol
Surface area2520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.878, 30.970, 43.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-8-

MN

DetailsThe author states that there is no possible quaternary structure

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Components

#1: DNA chain 5'-D(*CP*GP*TP*GP*CP*G)-3'


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O7P
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.99
Details: 50mM Sodium cacodylate, 5mM 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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2008 / Details: mirrors
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→15 Å / Num. all: 751 / Num. obs: 742 / % possible obs: 98.8 % / Redundancy: 3.83 % / Biso Wilson estimate: 40.616 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.0383 / Net I/σ(I): 8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.2377 / Mean I/σ(I) obs: 2 / Num. unique all: 82 / Rsym value: 0.2162 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→14.7 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.295 / SU ML: 0.188 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27015 41 5.6 %RANDOM
Rwork0.26859 ---
obs0.2687 693 99.73 %-
all-694 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.334 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2---0.45 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.15→14.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 121 4 6 131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021138
X-RAY DIFFRACTIONr_angle_refined_deg4.0563211
X-RAY DIFFRACTIONr_chiral_restr0.1280.223
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0264
X-RAY DIFFRACTIONr_nbd_refined0.2270.253
X-RAY DIFFRACTIONr_nbtor_refined0.3450.274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4510.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4590.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6880.23
LS refinement shellResolution: 2.153→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.066 1 -
Rwork0.358 55 -
obs-55 100 %

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