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- PDB-7bsg: Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanoclust... -

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Basic information

Entry
Database: PDB / ID: 7bsg
TitleCrystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (T5G mutant)
ComponentsDNA (5'-D(*CP*AP*CP*CP*GP*AP*GP*CP*GP*A)-3')
KeywordsDNA / Nanocluster / Silver
Function / homologySILVER ION / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKondo, J. / Cerretani, C. / Vosch, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: CrystEngComm / Year: 2020
Title: Mutation of position 5 as a crystal engineering tool for a NIR-emitting DNA-stabilized Ag16 nanocluster.
Authors: Cerretani, C. / Kondo, J. / Vosch, T.
History
DepositionMar 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*AP*CP*CP*GP*AP*GP*CP*GP*A)-3')
B: DNA (5'-D(*CP*AP*CP*CP*GP*AP*GP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,02020
Polymers6,0782
Non-polymers1,94218
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-134 kcal/mol
Surface area2570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.882, 33.677, 76.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 3039.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SF file contains Friedel pairs. / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
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: 1.59 Å3/Da / Density % sol: 22.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: MOPS, Spermine, calcium nitrate, PEG

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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 EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.19→22.35 Å / Num. obs: 3775 / % possible obs: 98.2 % / Redundancy: 3.147 % / Biso Wilson estimate: 29.535 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.158 / Χ2: 1.085 / Net I/σ(I): 5.47 / Num. measured all: 11879 / Scaling rejects: 75
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
2.19-2.252.6970.3192.558093053000.9080.40298.4
2.25-2.312.7710.2753.357152622580.9130.34598.5
2.31-2.382.8540.2633.217622732670.9510.32797.8
2.38-2.452.8430.2253.787252602550.9550.27798.1
2.45-2.532.8620.2024.697272572540.9430.24898.8
2.53-2.623.3460.1974.737832342340.9690.238100
2.62-2.723.3350.1945.277872372360.970.23399.6
2.72-2.833.4490.215.338382452430.9510.2599.2
2.83-2.963.4640.2254.967172082070.9520.26899.5
2.96-3.13.510.2344.647162062040.9260.27899
3.1-3.273.4380.1845.316601921920.9830.218100
3.27-3.473.370.1726.066201841840.9660.204100
3.47-3.713.2890.1666.725921981800.9750.19890.9
3.71-4.013.1370.1468.034361451390.9780.17795.9
4.01-4.393.3250.1376.795321611600.9870.16599.4
4.39-4.913.0160.1158.143861331280.9930.14296.2
4.91-5.673.1860.09610.134111291290.9740.116100
5.67-6.943.3220.09411.6328991870.9810.11395.6
6.94-9.813.1790.06911.8124881780.990.08396.3
9.81-22.353.150.06113.9112643400.9940.07393

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JR4

6jr4


Resolution: 2.19→22.35 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.02
RfactorNum. reflection% reflection
Rfree0.2466 365 9.67 %
Rwork0.2079 --
obs0.2116 3775 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.08 Å2 / Biso mean: 41.7302 Å2 / Biso min: 30.53 Å2
Refinement stepCycle: final / Resolution: 2.19→22.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 18 0 422
Biso mean--35.75 --
Num. residues----20
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.510.23191200.19911164128498
2.51-3.160.22431200.21781119123999
3.16-22.350.26681250.20661127125297

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