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- PDB-4xsn: Copper(II) bound to the Z-DNA form of d(CGCGCG) -

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Basic information

Entry
Database: PDB / ID: 4xsn
TitleCopper(II) bound to the Z-DNA form of d(CGCGCG)
ComponentsDNA (5'-D(*CP*(BGM)P*CP*GP*CP*GP)-3')
KeywordsDNA / Z-DNA / copper(II)
Function / homologyCOPPER (II) ION / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.452 Å
AuthorsRohner, M. / Medina-Molner, A. / Spingler, B.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Inorg.Chem. / Year: 2016
Title: N,N,O and N,O,N Meridional cis Coordination of Two Guanines to Copper(II) by d(CGCGCG)2.
Authors: Rohner, M. / Medina-Molner, A. / Spingler, B.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*(BGM)P*CP*GP*CP*GP)-3')
B: DNA (5'-D(*CP*(BGM)P*CP*GP*CP*GP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8423
Polymers3,7782
Non-polymers641
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint4 kcal/mol
Surface area2270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)18.799, 29.077, 43.278
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 DNA (5'-D(*CP*(BGM)P*CP*GP*CP*GP)-3')


Mass: 1889.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.59 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: cacodylate, MPD, calcium lactate, potassium chloride

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Data collection

DiffractionMean temperature: 183 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: STOE / Detector: IMAGE PLATE / Date: Dec 20, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.452→17.359 Å / Num. obs: 7657 / % possible obs: 100 % / Observed criterion σ(F): 4 / Redundancy: 1 % / Rmerge(I) obs: 0.0526 / Net I/σ(I): 14.46
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.3264 / Mean I/σ(I) obs: 4.3 / % possible all: 87.9

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Processing

Software
NameClassification
SHELXphasing
X-Areadata reduction
XSCALEdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.452→17.359 Å / Num. parameters: 2609 / Num. restraintsaints: 5420 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.157 378 4.937 %RANDOM
all0.121 7657 --
obs0.12 7657 100 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 341
Refinement stepCycle: LAST / Resolution: 1.452→17.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 248 0 98 346
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0131
X-RAY DIFFRACTIONs_angle_d0.367
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.003
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0186
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0089
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0216
X-RAY DIFFRACTIONs_approx_iso_adps0

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