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- PDB-7edw: DNA duplex containing T-T base pairs in complex with Au(III) -

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Basic information

Entry
Database: PDB / ID: 7edw
TitleDNA duplex containing T-T base pairs in complex with Au(III)
ComponentsDNA (5'-D(*GP*GP*AP*CP*CP*TP*TP*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 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 T-T base pairs in complex with Au(III)
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*TP*TP*GP*GP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*AP*CP*CP*TP*TP*GP*GP*TP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9005
Polymers7,3092
Non-polymers5913
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-24 kcal/mol
Surface area4320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.076, 42.800, 67.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AU / GOLD ION


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, gold 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: 1.03932 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03932 Å / Relative weight: 1
ReflectionResolution: 2→28.02 Å / Num. obs: 12947 / % possible obs: 92.5 % / Redundancy: 2.431 % / Biso Wilson estimate: 41.673 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.047 / Χ2: 2.288 / Net I/σ(I): 14.63 / Num. measured all: 31469
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
2-2.052.3170.3123.6225910559750.8140.38992.4
2.05-2.112.2720.2554.0521089969280.8810.3293.2
2.11-2.172.3360.2055.31225410069650.9360.25595.9
2.17-2.242.3650.1486.9320819208800.9630.18295.7
2.24-2.312.5330.1427.5422329328810.9710.17494.5
2.31-2.392.4270.1049.5520488928440.9890.12794.6
2.39-2.482.4950.09210.3620538688230.9910.11294.8
2.48-2.582.460.07912.1519268357830.9920.09793.8
2.58-2.72.3840.0713.1817007887130.9930.08690.5
2.7-2.832.4010.05416.717247677180.9950.06693.6
2.83-2.982.5330.04119.6816777086620.9970.0593.5
2.98-3.162.5850.03623.0116216826270.9970.04491.9
3.16-3.382.4770.03425.114766565960.9970.04290.9
3.38-3.652.3950.03326.9912916015390.9970.04189.7
3.65-42.3630.03227.2511465544850.9960.04187.5
4-4.472.4440.02529.310514854300.9980.0388.7
4.47-5.162.6320.02730.9110664514050.9980.03389.8
5.16-6.332.6160.02730.478323663180.9990.03286.9
6.33-8.952.3430.0330.355672832420.9980.03785.5
8.95-28.022.6840.03533.043571561330.9970.04285.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XSCALEdata scaling
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→28.02 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 1299 10.03 %
Rwork0.1648 11646 -
obs0.1671 12945 92.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.04 Å2 / Biso mean: 36.5332 Å2 / Biso min: 26.07 Å2
Refinement stepCycle: final / Resolution: 2→28.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 4 55 543
Biso mean--42.38 39.44 -
Num. residues----24
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.080.29951460.23611287143393
2.08-2.170.23451500.20481350150095
2.17-2.290.19621450.18741320146595
2.29-2.430.25051480.18421335148394
2.43-2.620.2341480.19161284143294
2.62-2.880.25821490.20981301145093
2.88-3.30.21811400.17531299143992
3.3-4.160.1281340.14361242137689
4.16-28.020.14381390.12881228136788

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