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

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Basic information

Entry
Database: PDB / ID: 7bsh
TitleCrystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (Abasic mutant)
ComponentsDNA (5'-D(*CP*AP*CP*CP*(3DR)P*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: 1.2 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*(3DR)P*AP*GP*CP*GP*A)-3')
B: DNA (5'-D(*CP*AP*CP*CP*(3DR)P*AP*GP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,72120
Polymers5,7802
Non-polymers1,94218
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-128 kcal/mol
Surface area2200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.223, 35.960, 43.482
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*(3DR)P*AP*GP*CP*GP*A)-3')


Mass: 2889.897 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.9 Å3/Da / Density % sol: 35.2 %
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 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→27.71 Å / Num. obs: 26773 / % possible obs: 99.9 % / Redundancy: 6.772 % / Biso Wilson estimate: 12.492 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.065 / Χ2: 1.178 / Net I/σ(I): 18.84 / Num. measured all: 181315 / Scaling rejects: 7
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
1.2-1.236.4760.2926.1912745198419680.9720.31899.2
1.23-1.266.5620.2457.2812672193119310.9830.266100
1.26-1.36.5370.2058.5412093185018500.9870.222100
1.3-1.346.4930.189.5612194187818780.9920.196100
1.34-1.386.0230.1679.9810565175617540.9890.18399.9
1.38-1.436.3320.1510.9110809170817070.9910.16499.9
1.43-1.497.1310.12112.7611923167216720.9970.131100
1.49-1.557.2280.10414.6111283156115610.9980.112100
1.55-1.627.2460.10315.7111181154315430.9980.111100
1.62-1.77.20.09717.5910353143914380.9980.10599.9
1.7-1.797.1390.08321.089873138313830.9980.089100
1.79-1.97.0680.06525.619344132213220.9980.07100
1.9-2.036.8810.05428.788470123112310.9980.059100
2.03-2.196.6220.04333.037509113411340.9990.047100
2.19-2.45.9560.03935.766290105710560.9990.04399.9
2.4-2.686.7870.03739.6564489519500.9990.0499.9
2.68-3.17.3880.03841.6662218428420.9990.041100
3.1-3.797.4120.03842.6452777137120.9990.04199.9
3.79-5.367.3250.03743.7539705425420.9990.04100
5.36-27.717.0070.03447.6620953032990.9990.03898.7

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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: 1.2→27.71 Å / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 6.68
RfactorNum. reflection% reflection
Rfree0.0884 2682 10.03 %
Rwork0.0772 --
obs0.0783 26741 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 37.36 Å2 / Biso mean: 16.8346 Å2 / Biso min: 9.31 Å2
Refinement stepCycle: final / Resolution: 1.2→27.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 382 18 33 433
Biso mean--10.37 23.31 -
Num. residues----20
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.220.10841330.11951214134798
1.22-1.240.10241420.10712841426100
1.24-1.270.08021420.091112811423100
1.27-1.30.09161400.084112581398100
1.3-1.330.08261410.077412621403100
1.33-1.360.07241440.071112751419100
1.36-1.40.07691410.074812771418100
1.4-1.440.11440.069312701414100
1.44-1.480.09041370.069212861423100
1.48-1.540.07381430.060312451388100
1.54-1.60.08511370.06711243138099
1.6-1.670.10241500.067112921442100
1.67-1.760.07971390.069412781417100
1.76-1.870.07791420.062712471389100
1.87-2.010.06871430.065212721415100
2.02-2.220.05611400.05912691409100
2.22-2.540.0731410.05912871428100
2.54-3.20.10191390.086412551394100
3.2-27.710.13251440.11571264140899

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