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- PDB-7ygp: DNA duplex containing 5OHU-T base pairs -

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Basic information

Entry
Database: PDB / ID: 7ygp
TitleDNA duplex containing 5OHU-T base pairs
ComponentsDNA (5'-D(*GP*GP*AP*CP*CP*TP*(OHU)P*GP*GP*TP*CP*C)-3')
KeywordsDNA / metal-mediated base pair / metallo-DNA / mercury
Function / homology: / COBALT HEXAMMINE(III) / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsKondo, J. / Torigoe, H. / Arakawa, F.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K19308 Japan
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA.
Authors: Torigoe, H. / Kondo, J. / Arakawa, F.
History
DepositionJul 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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*TP*(OHU)P*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8763
Polymers3,6561
Non-polymers2202
Water00
1
A: DNA (5'-D(*GP*GP*AP*CP*CP*TP*(OHU)P*GP*GP*TP*CP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,7536
Polymers7,3132
Non-polymers4404
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area1880 Å2
ΔGint-25 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.672, 36.672, 54.990
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 3656.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MPD, lithium chloride, hexammine cobalt chloride, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.00835 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00835 Å / Relative weight: 1
ReflectionResolution: 1.997→20.787 Å / Num. obs: 5348 / % possible obs: 95.1 % / Redundancy: 2.655 % / Biso Wilson estimate: 59.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.032 / Χ2: 1.987 / Net I/σ(I): 17.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.052.7030.3962.0711274494170.8420.48692.9
2.05-2.112.7080.2793.110293983800.9270.34295.5
2.11-2.172.7720.253.59593713460.9640.30593.3
2.17-2.232.650.1564.59783923690.9870.1994.1
2.23-2.312.6480.1136.689323783520.9890.13893.1
2.31-2.392.5620.0838.538613463360.9950.10297.1
2.39-2.482.7540.06511.049643633500.9970.07896.4
2.48-2.582.7550.04816.467993002900.9970.05896.7
2.58-2.72.8080.03917.469213423280.9990.04795.9
2.7-2.832.6720.03921.57993102990.9980.04796.5
2.83-2.982.6280.03525.446862712610.9980.04296.3
2.98-3.162.520.02429.496882832730.9990.02896.5
3.16-3.382.4590.02432.456002552440.9990.02995.7
3.38-3.652.5250.02334.756062552400.9990.02894.1
3.65-42.6780.02135.725572162080.9990.02596.3
4-4.472.7140.02437.364941921820.9980.0394.8
4.47-5.162.5740.02136.614351761690.9980.02696
5.16-6.322.4510.02536.033481501420.9980.03194.7
6.32-8.942.5370.02836.042741141080.9960.03794.7
8.94-20.7872.5930.02536.9414065540.9980.03283.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.997→20.787 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 41.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 529 9.91 %
Rwork0.2186 4807 -
obs0.2194 5336 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.24 Å2 / Biso mean: 60.4473 Å2 / Biso min: 47.66 Å2
Refinement stepCycle: final / Resolution: 1.997→20.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 242 8 0 250
Biso mean--85.42 --
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008276
X-RAY DIFFRACTIONf_angle_d1.153430
X-RAY DIFFRACTIONf_chiral_restr0.04546
X-RAY DIFFRACTIONf_plane_restr0.00512
X-RAY DIFFRACTIONf_dihedral_angle_d19.079110
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.997-2.19740.51471360.4347118493
2.1974-2.51490.39011290.3602118695
2.5149-3.16670.32721360.2924121896
3.1667-20.7870.16911280.1681121995

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