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- PDB-3ulo: X-ray Diffraction Studies of Ring Crystals obtained for d(CACGCG)... -

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Basic information

Entry
Database: PDB / ID: 3ulo
TitleX-ray Diffraction Studies of Ring Crystals obtained for d(CACGCG).d(CGCGTG): Stage (iv) Hexagonal rings
Components6-mer DNA
KeywordsDNA / Z-type DNA double helix / ring crystal / crystal morphology
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsMandal, P.K. / Venkadesh, S. / Gautham, N.
CitationJournal: J.Cryst.Growth / Year: 2012
Title: Ring crystals of oligonucleotides: Growth stages and X-ray diffraction studies
Authors: Mandal, P.K. / Chandrasekaran, A.R. / Madhanagopal, B.R. / Venkadesh, S. / Gautham, N.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 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
Revision 1.2Apr 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: 6-mer DNA
B: 6-mer DNA


Theoretical massNumber of molelcules
Total (without water)2,4442
Polymers2,4442
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-11 kcal/mol
Surface area1770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.670, 17.670, 42.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: DNA chain 6-mer DNA


Mass: 1221.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized by M/s Microsynth
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ACTUAL DNA SEQUENCE FOR THE THIS STUDY IS D(CACGCG).(CGCGTG)

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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: 1.576 Å3/Da / Density % sol: 21.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM DNA, 75mM sodium cacodylate trihydrate buffer (pH 7.0), 0.5mM cobalt hexammine chloride, 0.75mM 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: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 7, 2009 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.22→30 Å / Num. all: 250 / Num. obs: 237 / % possible obs: 94.8 % / Redundancy: 3.51 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.118 / Net I/σ(I): 3.4
Reflection shellResolution: 3.22→3.34 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 1.2 / Num. unique all: 37 / Rsym value: 0.318 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Z-type DNA tetranucleotide built using InsightII

Resolution: 3.24→14.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / SU B: 25.512 / SU ML: 0.418 / Cross valid method: THROUGHOUT / ESU R Free: 0.826 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE DNA OLIGONUCLEOTIDE HAS SIX BASE PAIRS (D(CACGCG).D(CGCGTG)) AND FORMS THE Z-TYPE DOUBLE HELICAL STRUCTURE. THE STRUCTURE HAS STATISTICAL DIS-ORDER AND THE ASYMMETRIC UNIT CONTAINS A ...Details: THE DNA OLIGONUCLEOTIDE HAS SIX BASE PAIRS (D(CACGCG).D(CGCGTG)) AND FORMS THE Z-TYPE DOUBLE HELICAL STRUCTURE. THE STRUCTURE HAS STATISTICAL DIS-ORDER AND THE ASYMMETRIC UNIT CONTAINS A TETRAMERIC DUPLEX WHICH COULD STAND FOR EITHER CPGPCPG/CPGPCPG OR CPAPCPG/CPGPTPG OR CPGPCPA/TPGPCPG. DUE TO DISORDER, THE TETRANUCLEOTIDE WAS CONSTRUCTED AS TPGPTPG/TPGPTPG IN WHICH THE C5 METHYL GROUP OF THYMINE WAS ASSIGNED OCCUPANCY OF 1/6 AND N2 OF GUANINE WAS ASSIGNED OCCUPANCY OF 5/6.
RfactorNum. reflection% reflectionSelection details
Rfree0.27652 14 6.1 %RANDOM
Rwork0.23783 ---
obs0.23984 215 95.02 %-
all-226 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.923 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 3.24→14.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 168 0 1 169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021186
X-RAY DIFFRACTIONr_angle_refined_deg1.5783284
X-RAY DIFFRACTIONr_chiral_restr0.0850.232
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0288
X-RAY DIFFRACTIONr_nbd_refined0.2540.292
X-RAY DIFFRACTIONr_nbtor_refined0.3010.289
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0510.21
X-RAY DIFFRACTIONr_scbond_it1.1493286
X-RAY DIFFRACTIONr_scangle_it1.4154.5284
LS refinement shellResolution: 3.242→3.321 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.694 2 -
Rwork0.508 16 -
obs-16 100 %

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