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- PDB-7edv: DNA duplex containing C-G-Au-C base triple -

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Basic information

Entry
Database: PDB / ID: 7edv
TitleDNA duplex containing C-G-Au-C base triple
ComponentsDNA (5'-D(*GP*GP*AP*CP*CP*CP*CP*GP*GP*TP*CP*C)-3')
KeywordsDNA / Metal-mediated base pair / Gold
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsKondo, J. / Iwase, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24245037 Japan
CitationJournal: To Be Published
Title: DNA duplex containing C-G-Au-C base triple
Authors: Kondo, J. / Iwase, E.
History
DepositionMar 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 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*CP*CP*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8212
Polymers3,6241
Non-polymers1971
Water66737
1
A: DNA (5'-D(*GP*GP*AP*CP*CP*CP*CP*GP*GP*TP*CP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)7,6434
Polymers7,2492
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_553-x,-x+y,-z-5/31
Buried area1430 Å2
ΔGint-14 kcal/mol
Surface area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.595, 38.595, 46.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-229-

HOH

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Components

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


Mass: 3624.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.59 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, lithium chloride

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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 PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.01→27.18 Å / Num. obs: 5183 / % possible obs: 100 % / Redundancy: 10.203 % / Biso Wilson estimate: 36.998 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.057 / Χ2: 2.227 / Net I/σ(I): 27.74 / Num. measured all: 52884
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.01-2.0610.1550.299.13540.980.306100
2.06-2.1210.1060.2510.973770.980.264100
2.12-2.1810.4440.18413.753740.990.193100
2.18-2.2510.430.14715.333700.9950.154100
2.25-2.329.5710.12917.063360.9940.136100
2.32-2.410.0860.10120.283370.9960.106100
2.4-2.4910.6990.08324.463060.9980.088100
2.49-2.5911.0550.07329.13070.9970.076100
2.59-2.7110.7990.07230.222930.9980.076100
2.71-2.8410.7790.06431.422810.9980.067100
2.84-2.9910.5290.0637.32800.9980.063100
2.99-3.1810.0570.04838.222640.9990.05100
3.18-3.399.0570.04640.882290.9990.049100
3.39-3.679.2380.04942.422100.9990.051100
3.67-4.0210.1050.04745.462100.9990.049100
4.02-4.4910.550.04247.731890.9980.044100
4.49-5.199.4970.04544.961610.9990.047100
5.19-6.359.2360.04345.441400.9990.045100
6.35-8.989.8290.04746.951050.9990.05100
8.98-27.1810.850.03350.926010.03596.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→27.18 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 538 10.38 %
Rwork0.1644 4645 -
obs0.1672 5183 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.79 Å2 / Biso mean: 27.4125 Å2 / Biso min: 18.36 Å2
Refinement stepCycle: final / Resolution: 2.01→27.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 1 37 278
Biso mean--24.96 34.09 -
Num. residues----12
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.210.25611320.21831154128699
2.21-2.530.21951300.189511591289100
2.53-3.180.23731380.184511661304100
3.19-27.180.14961380.13711661304100

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