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

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Basic information

Entry
Database: PDB / ID: 7bsf
TitleCrystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (T5C mutant)
ComponentsDNA (5'-D(*CP*AP*CP*CP*CP*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: 1.1 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*CP*AP*GP*CP*GP*A)-3')
B: DNA (5'-D(*CP*AP*CP*CP*CP*AP*GP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,98021
Polymers5,9982
Non-polymers1,98219
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-134 kcal/mol
Surface area2590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.958, 33.807, 52.523
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(*CP*AP*CP*CP*CP*AP*GP*CP*GP*A)-3')


Mass: 2998.984 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.77 Å3/Da / Density % sol: 30.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MOPS, Spermine, calcium nitrate, MPD

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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: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.1→28.43 Å / Num. obs: 33404 / % possible obs: 99.6 % / Redundancy: 6.812 % / Biso Wilson estimate: 7.906 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.097 / Χ2: 1.044 / Net I/σ(I): 14.1 / Num. measured all: 227563
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
1.1-1.136.1760.2755.4114939247724190.960.397.7
1.13-1.166.7770.2246.9316225240723940.9760.24299.5
1.16-1.196.8160.1868.2516100237923620.9840.20199.3
1.19-1.236.7350.1639.7515080225822390.9830.17799.2
1.23-1.276.7360.14910.4915062224622360.9880.16199.6
1.27-1.316.6490.13111.5314123212821240.990.14399.8
1.31-1.366.3870.12512.0213228207420710.9910.13699.9
1.36-1.426.0790.12111.9312091199219890.990.13299.8
1.42-1.487.0760.11813.3613550191519150.9930.127100
1.48-1.557.2370.10914.3413012179817980.9950.118100
1.55-1.647.2690.10515.1112568173017290.9940.11499.9
1.64-1.747.2420.09816.3111899164316430.9950.106100
1.74-1.867.1580.08719.1611116155315530.9950.094100
1.86-2.017.030.07520.8310004142314230.9960.081100
2.01-2.26.7360.06623.368912132313230.9970.072100
2.2-2.466.1580.0624.17291118411840.9960.066100
2.46-2.847.2850.0626.537649105010500.9970.065100
2.84-3.487.6250.06426.0668408978970.9970.069100
3.48-4.927.5920.06127.1852166876870.9980.065100
4.92-28.437.2230.05928.2426583703680.9980.06399.5

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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: 1.1→28.43 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 4.99
RfactorNum. reflection% reflection
Rfree0.0833 3354 10.04 %
Rwork0.0749 --
obs0.0757 33403 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 30 Å2 / Biso mean: 10.478 Å2 / Biso min: 4.47 Å2
Refinement stepCycle: final / Resolution: 1.1→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 398 19 47 464
Biso mean--5.73 17.28 -
Num. residues----20
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.110.12921410.12641239138098
1.12-1.130.10711340.09951227136198
1.13-1.150.09251420.089212331375100
1.15-1.170.0821400.08191245138598
1.17-1.190.06991420.072312531395100
1.19-1.210.06841390.06921234137399
1.21-1.230.07931410.062812291370100
1.23-1.260.07021460.06831282142899
1.26-1.290.07561390.06412531392100
1.29-1.320.0681440.064912421386100
1.32-1.350.07871390.060112611400100
1.35-1.380.06871350.061812521387100
1.39-1.430.07591410.062412631404100
1.43-1.470.06511380.057512451383100
1.47-1.520.07021400.05812691409100
1.52-1.590.09341440.060312831427100
1.59-1.660.08691330.066112221355100
1.66-1.740.08061410.073512771418100
1.74-1.850.08231420.067212481390100
1.85-20.06831420.071112581400100
2-2.20.07911400.063912581398100
2.2-2.520.05911360.065312481384100
2.52-3.170.11161420.093212711413100
3.17-28.430.12481330.122312571390100

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