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

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Basic information

Entry
Database: PDB / ID: 7xlw
TitleCrystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (G7I/G9I mutant)
ComponentsDNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
KeywordsDNA / Silver / nanocluster
Function / homologySILVER ION / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsKondo, J. / Cerretani, C. / Vosch, T.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research0136-00024B Denmark
CitationJournal: Nanoscale Adv / Year: 2022
Title: The effect of inosine on the spectroscopic properties and crystal structure of a NIR-emitting DNA-stabilized silver nanocluster.
Authors: Cerretani, C. / Liisberg, M.B. / Ruck, V. / Kondo, J. / Vosch, T.
History
DepositionApr 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
B: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
C: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
D: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
E: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
F: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
G: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
H: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
I: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
J: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
K: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
L: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,457120
Polymers35,80812
Non-polymers11,650108
Water2,126118
1
A: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
B: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91020
Polymers5,9682
Non-polymers1,94218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
D: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91020
Polymers5,9682
Non-polymers1,94218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
F: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91020
Polymers5,9682
Non-polymers1,94218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
H: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91020
Polymers5,9682
Non-polymers1,94218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
J: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91020
Polymers5,9682
Non-polymers1,94218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
L: DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91020
Polymers5,9682
Non-polymers1,94218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.232, 49.663, 55.885
Angle α, β, γ (deg.)74.030, 90.370, 83.730
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 9)
21(chain B and resid 1 through 9)
31(chain C and resid 1 through 9)
41(chain D and resid 1 through 9)
51(chain E and resid 1 through 9)
61chain F
71(chain G and resid 1 through 9)
81(chain H and resid 1 through 9)
91(chain I and resid 1 through 9)
101(chain J and resid 1 through 9)
111(chain K and resid 1 through 9)
121(chain L and resid 1 through 9)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DI / End label comp-ID: DI / Auth seq-ID: 1 - 9 / Label seq-ID: 1 - 9

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 1 through 9)AA
2(chain B and resid 1 through 9)BB
3(chain C and resid 1 through 9)CC
4(chain D and resid 1 through 9)DD
5(chain E and resid 1 through 9)EE
6chain FFF
7(chain G and resid 1 through 9)GG
8(chain H and resid 1 through 9)HH
9(chain I and resid 1 through 9)II
10(chain J and resid 1 through 9)JJ
11(chain K and resid 1 through 9)KK
12(chain L and resid 1 through 9)LL

NCS ensembles :
ID
1
2

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Components

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


Mass: 2983.967 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical...
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 108 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: MPD, spermine, ammonium nitrate, MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.89→41.76 Å / Num. obs: 22032 / % possible obs: 95.3 % / Redundancy: 3.645 % / Biso Wilson estimate: 19.017 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.098 / Χ2: 0.912 / Net I/σ(I): 10.78 / Num. measured all: 80305 / Scaling rejects: 4
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
1.89-1.943.6310.3773.185704169115710.9280.44392.9
1.94-23.660.2883.975815168115890.9590.33894.5
2-2.053.5910.234.825387159815000.970.27193.9
2.05-2.123.4580.166.15049156914600.9880.19193.1
2.12-2.193.3210.1277.34775155214380.9890.15392.7
2.19-2.263.1170.1038.624189147713440.9910.12591
2.26-2.353.3380.08310.464153141912440.9950.09987.7
2.35-2.443.4970.07711.734574134513080.9960.09197.2
2.44-2.553.8880.08212.315078134113060.9960.09597.4
2.55-2.683.890.07713.44688123512050.9960.0997.6
2.68-2.823.8980.08712.464685123112020.9950.10197.6
2.82-2.993.8860.09711.934244111110920.9920.11298.3
2.99-3.23.890.09711.164077106910480.9950.11298
3.2-3.463.8570.08612.3137459869710.9970.198.5
3.46-3.793.8550.07115.4534199028870.9960.08398.3
3.79-4.233.830.06516.9431678378270.9960.07598.8
4.23-4.893.8230.05918.5227147117100.9960.06999.9
4.89-5.993.7680.0521.9723026206110.9960.05898.5
5.99-8.473.6840.03628.5617134724650.9980.04298.5
8.47-41.763.2560.02632.588272602540.9980.0397.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JR4

6jr4


Resolution: 1.89→41.76 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 19.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1826 1995 9.08 %
Rwork0.15 19984 -
obs0.1529 21979 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.33 Å2 / Biso mean: 28.6803 Å2 / Biso min: 14.25 Å2
Refinement stepCycle: final / Resolution: 1.89→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2355 108 118 2581
Biso mean--22.18 27.99 -
Num. residues----119
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A888X-RAY DIFFRACTION4.958TORSIONAL
12B888X-RAY DIFFRACTION4.958TORSIONAL
13C888X-RAY DIFFRACTION4.958TORSIONAL
14D888X-RAY DIFFRACTION4.958TORSIONAL
15E888X-RAY DIFFRACTION4.958TORSIONAL
16F888X-RAY DIFFRACTION4.958TORSIONAL
17G888X-RAY DIFFRACTION4.958TORSIONAL
18H888X-RAY DIFFRACTION4.958TORSIONAL
19I888X-RAY DIFFRACTION4.958TORSIONAL
110J888X-RAY DIFFRACTION4.958TORSIONAL
111K888X-RAY DIFFRACTION4.958TORSIONAL
112L888X-RAY DIFFRACTION4.958TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.940.24611370.2371367150492
1.94-1.990.23171440.20361437158194
1.99-2.050.20941380.19031383152194
2.05-2.120.1721370.16261380151793
2.12-2.190.18761400.15041404154493
2.19-2.280.19011350.14241345148090
2.28-2.380.1541370.13041367150490
2.38-2.510.15971460.11951446159297
2.51-2.670.15391460.12251463160997
2.67-2.870.16371470.14391483163098
2.87-3.160.23111470.17491473162098
3.16-3.620.22821450.18521466161198
3.62-4.560.21751480.15971485163399
4.56-41.760.12651480.11331485163399

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