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- PDB-9kcc: DNA duplex containing copper-mediated 5-fluorouracil-cytosine bas... -

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Basic information

Entry
Database: PDB / ID: 9kcc
TitleDNA duplex containing copper-mediated 5-fluorouracil-cytosine base pairs
ComponentsDNA (5'-D(*GP*GP*AP*CP*CP*CP*(UFP)P*GP*GP*TP*CP*C)-3')
KeywordsDNA / metal-mediated base pair / copper / 5-fluorouracil
Function / homologyCOPPER (II) ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsKondo, J. / Hirabayashi, K. / Torigoe, H. / Adachi, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Dalton Trans / Year: 2025
Title: Novel specific binding of copper ions to naturally modified base pairs involving 5-fluorouracil in duplex DNA.
Authors: Torigoe, H. / Hirabayashi, K. / Adachi, S. / Kondo, J.
History
DepositionNov 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*AP*CP*CP*CP*(UFP)P*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7072
Polymers3,6431
Non-polymers641
Water00
1
A: DNA (5'-D(*GP*GP*AP*CP*CP*CP*(UFP)P*GP*GP*TP*CP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*AP*CP*CP*CP*(UFP)P*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4144
Polymers7,2872
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2690 Å2
ΔGint-22 kcal/mol
Surface area3990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.467, 39.467, 74.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain DNA (5'-D(*GP*GP*AP*CP*CP*CP*(UFP)P*GP*GP*TP*CP*C)-3')


Mass: 3643.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
Has ligand of interestY
Has protein modificationN

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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: 3.99 Å3/Da / Density % sol: 69.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MPD, MOPS, Spermine, Copper chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.37776 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37776 Å / Relative weight: 1
ReflectionResolution: 2.31→27.96 Å / Num. obs: 4875 / % possible obs: 91.7 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.042 / Net I/σ(I): 7.19
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.31-2.450.6117510.6340.8361
2.45-2.620.2836990.9330.3841
2.62-2.820.126580.9840.1591
2.82-3.090.046070.9980.0521
3.09-3.460.0295560.9980.0381
3.46-3.980.0314690.9970.041
3.98-4.870.0283740.9980.0361
4.87-6.830.0342960.9930.0451
6.83-27.960.0241470.9970.0341

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Modeller

Resolution: 2.31→27.1 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 242 4.96 %
Rwork0.1904 --
obs0.1914 4875 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 241 1 0 242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.115
X-RAY DIFFRACTIONf_dihedral_angle_d11.312110
X-RAY DIFFRACTIONf_chiral_restr0.04846
X-RAY DIFFRACTIONf_plane_restr0.00612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.910.4421170.39942319X-RAY DIFFRACTION99
2.91-27.10.18881250.16922314X-RAY DIFFRACTION99

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