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- PDB-7eay: DNA containing Cu(II)-mediated 4-N-carboxymethylcytosine base pairs -

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Basic information

Entry
Database: PDB / ID: 7eay
TitleDNA containing Cu(II)-mediated 4-N-carboxymethylcytosine base pairs
ComponentsDNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
KeywordsDNA / metal-mediated base pair
Function / homology: / COPPER (II) ION / : / COBALT HEXAMMINE(III) / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKondo, J. / Terashima, A. / Yoshimura, A. / Tada, Y. / Ono, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24245037 Japan
CitationJournal: To Be Published
Title: DNA containing Cu(II)-mediated 4-N-carboxymethylcytosine base pairs
Authors: Kondo, J. / Terashima, A. / Yoshimura, A. / Tada, Y. / Ono, A.
History
DepositionMar 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: 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*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
C: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
E: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
G: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
H: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
I: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
J: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
K: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,60246
Polymers44,88512
Non-polymers3,71734
Water1,72996
1
A: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
C: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,12015
Polymers14,9624
Non-polymers1,15811
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-71 kcal/mol
Surface area9150 Å2
MethodPISA
2
E: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
G: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
H: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,26116
Polymers14,9624
Non-polymers1,29912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-72 kcal/mol
Surface area8890 Å2
MethodPISA
3
I: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
J: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
K: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
L: DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,22215
Polymers14,9624
Non-polymers1,26011
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-73 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.923, 155.333, 80.627
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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DNA chain , 1 types, 12 molecules ABCDEFGHIJKL

#1: DNA chain
DNA (5'-D(*GP*GP*AP*CP*CP*(J0X)P*(J0X)P*GP*GP*TP*CP*C)-3')


Mass: 3740.428 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 130 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MPD, hexamine cobalt chloride, potassium 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: 0.98 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→39.27 Å / Num. obs: 37324 / % possible obs: 99.3 % / Redundancy: 3.373 % / Biso Wilson estimate: 54.663 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.068 / Χ2: 1.171 / Net I/σ(I): 12.46 / Num. measured all: 125895
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
2.5-2.573.4770.3813.349590280827580.9290.44998.2
2.57-2.643.5230.3293.819527270927040.9370.38899.8
2.64-2.723.4770.2325.199026259925960.9720.27499.9
2.72-2.83.3240.1845.818545257125710.9790.219100
2.8-2.893.4540.1527.088598249124890.9860.1899.9
2.89-2.993.3590.1158.868035239423920.9890.13799.9
2.99-3.113.520.08311.238134231423110.9960.09799.9
3.11-3.233.4490.06513.467723224922390.9960.07799.6
3.23-3.383.3060.05115.446920210120930.9970.06199.6
3.38-3.543.2260.05615.846623207020530.9960.06799.2
3.54-3.733.2330.05416.766204193919190.9960.06599
3.73-3.963.4110.05217.646062178917770.9970.06299.3
3.96-4.233.3710.04719.35869175117410.9970.05699.4
4.23-4.573.2040.04619.765117161115970.9960.05599.1
4.57-5.013.3040.04420.214883149814780.9980.05298.7
5.01-5.63.4510.04321.054497131213030.9990.05199.3
5.6-6.473.2050.04520.183747117911690.9970.05499.2
6.47-7.923.1810.04121.3331309969840.9970.04998.8
7.92-11.23.2660.03923.1924957777640.9980.04798.3
11.2-39.273.0310.03523.411704213860.9980.04291.7

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.69 / FOM acentric: 0.71 / FOM centric: 0.53 / Reflection: 9436 / Reflection acentric: 8186 / Reflection centric: 1250
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-9.20.690.710.5812891046243
4.6-5.70.70.720.5416061383223
4-4.60.710.740.515791387192
3.4-40.680.70.4927992503296
3.2-3.40.650.670.3717171564153

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SOLVEphasing
PHENIX1.17.1refinement
XSCALEdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→39.27 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 3713 9.97 %
Rwork0.2141 33538 -
obs0.2181 37251 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.03 Å2 / Biso mean: 48.4471 Å2 / Biso min: 23.86 Å2
Refinement stepCycle: final / Resolution: 2.5→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2976 136 96 3208
Biso mean--64.7 42.88 -
Num. residues----144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.540.43381320.3711171130396
2.54-2.570.35081370.32413101447100
2.57-2.60.40881160.325212201336100
2.6-2.640.35511400.333812921432100
2.64-2.680.38981410.270112291370100
2.68-2.720.38791360.296512491385100
2.72-2.770.30841440.275212331377100
2.77-2.810.34461290.261212861415100
2.81-2.870.3121420.26612511393100
2.87-2.920.311440.272112251369100
2.92-2.980.28371490.281412591408100
2.98-3.050.30181360.283112041340100
3.05-3.120.30441500.236312821432100
3.12-3.190.31241430.225912421385100
3.19-3.280.21661330.18921197133099
3.28-3.380.30711340.19741256139098
3.38-3.490.2821410.20131238137999
3.49-3.610.25951330.22651241137499
3.61-3.750.24511380.22041247138599
3.76-3.930.23741430.20021254139799
3.93-4.130.21921290.16881211134099
4.13-4.390.23221420.184612561398100
4.39-4.730.20761380.17861253139199
4.73-5.20.23561330.17691235136899
5.21-5.960.18071390.17531250138999
5.96-7.490.2291380.19491236137499
7.5-39.270.16391330.20211211134496

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