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- PDB-3v9d: Crystal structure of the tetra-decanucleotide d(CCCCGGTACCGGGG)2 ... -

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Basic information

Entry
Database: PDB / ID: 3v9d
TitleCrystal structure of the tetra-decanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex
ComponentsDNA (5'-D(*CP*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*GP*G)-3')
KeywordsDNA / Tetra-decanucleotide / A-DNA duplex / Crystal packing / A-type double helix
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMandal, P.K. / Venkadesh, S. / Gautham, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex
Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N.
History
DepositionDec 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,6203
Polymers8,5662
Non-polymers551
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-8 kcal/mol
Surface area5160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.340, 29.340, 87.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 4282.768 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 12mM MnCl2, 10mM spermine, equilibrated against 50 % methyl pentane diol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 28, 2011 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→29.34 Å / Num. all: 2606 / Num. obs: 2599 / % possible obs: 99.7 % / Redundancy: 4.64 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.042 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.69 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 1.5 / Num. unique all: 253 / Rsym value: 0.272 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0109refinement
AUTOMARdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A-DNA duplex Fiber model (tetra-decanucleotide) built using Insight-II

Resolution: 2.5→29.34 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU ML: 0.252 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.252 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Molecular replacement was carried out using AMoRe [Navaza, 1994] of the CCP4 suite. The A-DNA duplex gave the best correlation coefficient (83%)
RfactorNum. reflection% reflectionSelection details
Rfree0.24435 113 4.4 %RANDOM
Rwork0.21651 ---
obs0.21783 2449 99.3 %-
all-2467 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.3799 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 568 1 15 584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021636
X-RAY DIFFRACTIONr_angle_refined_deg3.2163978
X-RAY DIFFRACTIONr_chiral_restr0.1220.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02294
X-RAY DIFFRACTIONr_scbond_it2.2813636
X-RAY DIFFRACTIONr_scangle_it3.4274.5978
LS refinement shellResolution: 2.501→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 7 -
Rwork0.468 173 -
obs--98.9 %

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