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

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Basic information

Entry
Database: PDB / ID: 3ulm
TitleX-ray Diffraction Studies of Ring Crystals obtained for d(CACGCG).d(CGCGTG): Stage (ii) Hexagonal plates with spots
Components6-mer DNA
KeywordsDNA / Z-type DNA double helix
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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

Downloads & links

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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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.489, 17.489, 41.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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

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: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.54 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 26, 2009
Details: The optics consist in a vertical collimating mirror, a double-crystal Si(111) monochromator followed by a toroidal bendable focussing mirror.
RadiationMonochromator: a double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 147 / Num. obs: 147 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.0947 / Net I/σ(I): 3.3
Reflection shellResolution: 3.01→3.12 Å / Redundancy: 6.67 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1 / Num. unique all: 12 / Rsym value: 0.352 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Z-type DNA Dinucleotide step built using InsightII

Resolution: 3.01→15.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.835 / SU B: 16.392 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 / 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 COMPRISES OF A DINUCLEOTIDE STEP ...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 COMPRISES OF A DINUCLEOTIDE STEP IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE DINUCLEOTIDE STEP COULD STAND FOR EITHER CPG/CPG OR CPA/TPG. DUE TO DISORDER, THE DINUCLEOTIDE STEP WAS CONSTRUCTED AS TPG/TPG WHERE 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
Rfree0.23283 10 6.9 %RANDOM
Rwork0.19618 ---
obs0.19924 135 98.64 %-
all-145 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.785 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 3.01→15.15 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 81 0 1 82
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02189
X-RAY DIFFRACTIONr_angle_refined_deg3.9393134
X-RAY DIFFRACTIONr_chiral_restr0.1810.215
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0244
X-RAY DIFFRACTIONr_scbond_it2.307389
X-RAY DIFFRACTIONr_scangle_it3.7264.5134
LS refinement shellResolution: 3.013→3.088 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.384 8 -
obs-8 100 %

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