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- PDB-7xkm: Crystal structure of DNA-Ag(I) rod comprising a one-dimensional a... -

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Basic information

Entry
Database: PDB / ID: 7xkm
TitleCrystal structure of DNA-Ag(I) rod comprising a one-dimensional array of 11 silver ions
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3')
KeywordsDNA / Silver / Rod
Function / homologySILVER ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å
AuthorsKondo, J. / Ono, A. / Atsugi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H03033 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: A Novel Ag I -DNA Rod Comprising a One-Dimensional Array of 11 Silver Ions within a Double Helical Structure.
Authors: Atsugi, T. / Ono, A. / Tasaka, M. / Eguchi, N. / Fujiwara, S. / Kondo, J.
History
DepositionApr 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 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(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,46127
Polymers14,9804
Non-polymers2,48123
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-129 kcal/mol
Surface area5190 Å2
Unit cell
Length a, b, c (Å)77.461, 77.461, 123.722
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain
DNA (5'-D(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3')


Mass: 3745.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical...
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MPD, spermine, MOPS, lithium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.91973 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91973 Å / Relative weight: 1
ReflectionResolution: 2.79→36.96 Å / Num. obs: 10286 / % possible obs: 99.9 % / Redundancy: 21.109 % / Biso Wilson estimate: 41.924 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.117 / Χ2: 1.275 / Net I/σ(I): 22.55
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
2.8-2.8719.6350.25710.43150017677640.9970.26499.6
2.87-2.9521.7360.3449.07157157237230.9940.352100
2.95-3.0321.7510.29110.92159007317310.9950.298100
3.03-3.1321.5330.23912.78148796916910.9960.244100
3.13-3.2321.4960.20814.01147686876870.9980.213100
3.23-3.3421.4720.22213.6140006526520.9970.227100
3.34-3.4720.6850.23913.53131976386380.9960.245100
3.47-3.6120.0690.16617.75122226096090.9980.17100
3.61-3.7720.490.14820.4118235775770.9990.151100
3.77-3.9521.8460.13524.03124525705700.9990.138100
3.95-4.1722.0170.11926.48117575345340.9990.122100
4.17-4.4221.8350.12525.69108524974970.9990.128100
4.42-4.7221.5760.11927.51102704764760.9990.122100
4.72-5.120.3940.13624.3690144434420.9980.1499.8
5.1-5.5919.8840.10331.180534054050.9990.106100
5.59-6.2521.5260.08737.3577283593590.9990.089100
6.25-7.2221.8170.05752.78715632832810.058100
7.22-8.8420.8710.0465.59567727227210.041100
8.84-12.519.4070.03570.67415321421410.036100
12.5-36.9621.470.02686.29251211911710.02798.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.79→36.96 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1037 10.09 %
Rwork0.1869 9237 -
obs0.1901 10274 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.15 Å2 / Biso mean: 46.1664 Å2 / Biso min: 30.37 Å2
Refinement stepCycle: final / Resolution: 2.79→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 956 23 6 985
Biso mean--49.77 34.19 -
Num. residues----48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.79-2.940.22941440.19391306145099
2.94-3.130.25711440.184613291473100
3.13-3.370.24171530.199913311484100
3.37-3.710.28141530.197312991452100
3.71-4.240.17671530.182313251478100
4.24-5.340.26081400.206113211461100
5.34-36.960.15841500.16713261476100

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