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- PDB-7ygo: DNA duplex containing 5OHU-Hg(II)-T base pairs -

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Basic information

Entry
Database: PDB / ID: 7ygo
TitleDNA duplex containing 5OHU-Hg(II)-T base pairs
ComponentsDNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3')
KeywordsDNA / metal-mediated base pair / metallo-DNA / mercury
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 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*(6HU)P*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8572
Polymers3,6561
Non-polymers2011
Water00
1
A: DNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7144
Polymers7,3132
Non-polymers4012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557-x,-x+y,-z+7/31
Buried area1510 Å2
ΔGint-68 kcal/mol
Surface area4270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.336, 37.336, 54.938
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*(6HU)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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MPD, spermine, potassium nitrate, MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.0091 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0091 Å / Relative weight: 1
ReflectionResolution: 2.4→27.866 Å / Num. obs: 3345 / % possible obs: 99.8 % / Redundancy: 10.032 % / Biso Wilson estimate: 71.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.038 / Χ2: 1.568 / Net I/σ(I): 30.95 / Num. measured all: 33557 / Scaling rejects: 11
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
2.4-2.478.8860.3044.724262762730.9920.32398.9
2.47-2.5410.1720.2716.623092272270.9880.285100
2.54-2.6210.0710.1858.9725482532530.9960.195100
2.62-2.710.4740.14212.0325872472470.9970.15100
2.7-2.810.9780.12114.1924482242230.9980.12799.6
2.8-2.9110.9070.09318.627052482480.9990.098100
2.91-3.0210.8030.04930208519319310.051100
3.02-3.1610.5350.04435.0822652152150.9990.047100
3.16-3.3110.2020.03440.24196919319310.035100
3.31-3.499.3810.03542.57165117617610.038100
3.49-3.79.2840.03550.09176419019010.037100
3.7-3.969.3960.03346.97144715415410.034100
3.96-4.2810.1550.03754.35163516116110.039100
4.28-4.699.9220.03355.7215281541540.9990.034100
4.69-5.2410.0170.03558.5711621161160.9990.036100
5.24-6.059.6190.03156.9410871131130.9990.032100
6.05-7.418.80.0355.0888010010010.032100
7.41-10.489.4030.02955.82677727210.031100
10.48-27.86610.3780.03162.1438440370.9990.03392.5

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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: 2.403→27.866 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 337 10.1 %
Rwork0.2045 2999 -
obs0.2078 3336 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.16 Å2 / Biso mean: 72.6245 Å2 / Biso min: 60.81 Å2
Refinement stepCycle: final / Resolution: 2.403→27.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 242 1 0 243
Biso mean--81.86 --
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008270
X-RAY DIFFRACTIONf_angle_d0.939415
X-RAY DIFFRACTIONf_chiral_restr0.04146
X-RAY DIFFRACTIONf_plane_restr0.00512
X-RAY DIFFRACTIONf_dihedral_angle_d17.02110
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.403-3.02650.3041650.2808149299
3.0265-27.8660.22411720.19081507100

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