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- PDB-3tci: Crystal structure of the decameric sequence d(CGGGCGCCCG) as Z ty... -

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Basic information

Entry
Database: PDB / ID: 3tci
TitleCrystal structure of the decameric sequence d(CGGGCGCCCG) as Z type duplex
Components(DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')) x 2
KeywordsDNA / Z-DNA duplex
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.421 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Gautham, N.
CitationJournal: To be Published
Title: Crystal structure of the decameric sequence d(CGGGCGCCCG) as Z type duplex
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionAug 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')
C: DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,7674
Polymers4,7674
Non-polymers00
Water905
1
A: DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)2,3842
Polymers2,3842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)2,3842
Polymers2,3842
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.767, 17.767, 42.060
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 DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: DNA chain DNA (5'-D(P*CP*GP*GP*GP*CP*GP*CP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 7
Details: 1mM DNA, 2M MgCl2, 1mM spermine, 50% MPD , pH 7.0, 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: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 2, 2009 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.41→30 Å / Num. all: 586 / Num. obs: 579 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.41 % / Biso Wilson estimate: 54.506 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.053 / Net I/σ(I): 4.4
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 3.51 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 1.7 / Num. unique all: 63 / Rsym value: 0.224 / % possible all: 96.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
PHENIX(phenix.refine: 1.6_289)refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.421→15.387 Å / SU ML: 0.33 / σ(F): 1.72 / Phase error: 28.16 / Stereochemistry target values: LS_WUNIT_K1
Details: The sequence is d(CGGGCGCCCG). The molecule is placed in three-fold screw axis and form pseudo-continuous helix (Z-type) along c-axis. For this reason, the crystallographic asymmetric unit ...Details: The sequence is d(CGGGCGCCCG). The molecule is placed in three-fold screw axis and form pseudo-continuous helix (Z-type) along c-axis. For this reason, the crystallographic asymmetric unit consist of two tetramers such as d(CGCG) in 80% and d(GCGC) in 20%.
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 16 2.92 %Random
Rwork0.183 ---
all0.1838 586 --
obs0.1838 548 95.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 172.268 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4407 Å20 Å20 Å2
2---0.4407 Å2-0 Å2
3---0.8815 Å2
Refinement stepCycle: LAST / Resolution: 2.421→15.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 0 5 327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006358
X-RAY DIFFRACTIONf_angle_d1.603544
X-RAY DIFFRACTIONf_dihedral_angle_d31.156146
X-RAY DIFFRACTIONf_chiral_restr0.0662
X-RAY DIFFRACTIONf_plane_restr0.00316
LS refinement shellHighest resolution: 2.4213 Å
RfactorNum. reflection% reflection
Rfree0.1992 16 -
Rwork0.183 532 -
obs--95 %

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