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- PDB-3gcy: Crystal studies of d(CACGCG).d(CGCGTG) grown in presence of calci... -

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Basic information

Entry
Database: PDB / ID: 3gcy
TitleCrystal studies of d(CACGCG).d(CGCGTG) grown in presence of calcium chloride
Components
  • 5'-D(*CP*AP*CP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*GP*TP*G)-3'
KeywordsDNA / Z-form DNA duplex with Watson-Crick base pairing
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMandal, P.K. / Venkadesh, S. / Nandini, M. / Gautham, N.
CitationJournal: To be Published
Title: Crystal studies of d(CACGCG).d(CGCGTG) grown with various metal ions
Authors: Mandal, P.K. / Venkadesh, S. / Nandini, M. / Gautham, N.
History
DepositionFeb 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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 1.3Apr 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: 5'-D(*CP*AP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)3,6192
Polymers3,6192
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-6 kcal/mol
Surface area2320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.388, 30.618, 44.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*CP*GP*TP*G)-3'


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.64 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.99
Details: Sodium Cacodylate 50mM, Calcium chloride 140mM, Spermine 1mM, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium cacoldylate11
2Calcium chloride11
3Spermine11
4Sodium cacoldylate12
5Calcium chloride12

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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: Feb 14, 2009 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 2431 / Num. obs: 2334 / % possible obs: 95.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.37 Å2 / Rmerge(I) obs: 0.1026 / Rsym value: 0.0888 / Net I/σ(I): 4.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.27 % / Rmerge(I) obs: 0.3416 / Mean I/σ(I) obs: 1.3 / Num. unique all: 226 / Rsym value: 0.2905 / % possible all: 99.1

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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-DNA FIBER MODEL BUILT WITH INSIGHT-II

Resolution: 1.8→15.12 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.213 / SU ML: 0.14 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23339 114 4.9 %RANDOM
Rwork0.22812 ---
obs0.22845 2216 95.96 %-
all-2309 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.708 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 246 0 36 282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021276
X-RAY DIFFRACTIONr_angle_refined_deg2.0873426
X-RAY DIFFRACTIONr_chiral_restr0.0670.248
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02125
X-RAY DIFFRACTIONr_nbd_refined0.180.2110
X-RAY DIFFRACTIONr_nbtor_refined0.2870.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2630.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.27
X-RAY DIFFRACTIONr_scbond_it2.1723395
X-RAY DIFFRACTIONr_scangle_it2.1964.5424
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.652 6 -
Rwork0.356 163 -
obs-163 100 %

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