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

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Basic information

Entry
Database: PDB / ID: 7bse
TitleCrystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (T5A mutant)
ComponentsDNA (5'-D(*CP*AP*CP*CP*AP*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: 1.5 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 / struct_ncs_dom_lim
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,29648
Polymers12,0924
Non-polymers4,20444
Water1,71195
1
A: DNA (5'-D(*CP*AP*CP*CP*AP*AP*GP*CP*GP*A)-3')
B: DNA (5'-D(*CP*AP*CP*CP*AP*AP*GP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,18825
Polymers6,0462
Non-polymers2,14223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-91 kcal/mol
Surface area3400 Å2
MethodPISA
2
C: DNA (5'-D(*CP*AP*CP*CP*AP*AP*GP*CP*GP*A)-3')
D: DNA (5'-D(*CP*AP*CP*CP*AP*AP*GP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,10823
Polymers6,0462
Non-polymers2,06221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-91 kcal/mol
Surface area3420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.353, 45.353, 82.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11D-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DC / Beg label comp-ID: DC / End auth comp-ID: DA / End label comp-ID: DA / Auth seq-ID: 1 - 10 / Label seq-ID: 1 - 10

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

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


Mass: 3023.009 Da / Num. of mol.: 4 / 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.: 36 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.76 Å3/Da / Density % sol: 30.07 %
Crystal growTemperature: 293 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: 1.5→32.07 Å / Num. obs: 26478 / % possible obs: 99.7 % / Redundancy: 13.857 % / Biso Wilson estimate: 15.074 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.114 / Χ2: 1.077 / Net I/σ(I): 17.16 / Num. measured all: 366916 / Scaling rejects: 153
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
1.5-1.5413.7880.3927.4326542196619250.9930.40797.9
1.54-1.5814.3730.3298.7527553192219170.9930.34199.7
1.58-1.6214.3380.2599.9426740187818650.9980.26999.3
1.62-1.6714.4440.27710.7125797178917860.9940.28799.8
1.67-1.7314.3370.24411.9924989174717430.9970.25399.8
1.73-1.7914.3030.20813.5624158169016890.9970.21699.9
1.79-1.8614.1820.171523343164716460.9970.17699.9
1.86-1.9313.5980.17415.7621158156215560.9980.18199.6
1.93-2.0213.7060.13316.8720997153315320.9980.13999.9
2.02-2.1212.8750.11219.4518475143914350.9980.11799.7
2.12-2.2312.5920.09621.417226136913680.9980.10199.9
2.23-2.3711.1970.08722.7514634130913070.9970.09299.8
2.37-2.5312.4720.08225.2114954119911990.9990.086100
2.53-2.7314.3010.0827.0916417114811480.9990.082100
2.73-2.9914.8580.07727.115437103910390.9990.08100
2.99-3.3514.8690.08225.79141409519510.9990.085100
3.35-3.8714.4620.07828.63118598208200.9980.081100
3.87-4.7314.6540.07126.51104487157130.9990.07499.7
4.73-6.714.8590.06228.1802454054010.064100
6.7-32.0713.4620.05328.0240253012990.9990.05699.3

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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: 1.5→32.07 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.12
RfactorNum. reflection% reflection
Rfree0.1373 2639 10.04 %
Rwork0.1243 --
obs0.1257 26283 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 43.83 Å2 / Biso mean: 14.4708 Å2 / Biso min: 6.57 Å2
Refinement stepCycle: final / Resolution: 1.5→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 804 44 95 943
Biso mean--11.22 19.94 -
Num. residues----40
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A384X-RAY DIFFRACTION14.695TORSIONAL
12B384X-RAY DIFFRACTION14.695TORSIONAL
13C384X-RAY DIFFRACTION14.695TORSIONAL
14D384X-RAY DIFFRACTION14.695TORSIONAL
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 (%)
1.5-1.520.15351380.16271207134595
1.52-1.550.17951390.131112611400100
1.55-1.590.19581370.125812371374100
1.59-1.620.14151390.12331238137798
1.62-1.660.1661390.124712621401100
1.66-1.70.14591370.120912411378100
1.7-1.740.13431410.1112891430100
1.74-1.80.13571390.116612201359100
1.8-1.850.13851330.122412381371100
1.85-1.920.15121470.134512751422100
1.92-20.15521270.12581245137299
2-2.090.13691340.11111235136997
2.09-2.20.11791410.10951222136398
2.2-2.340.12461410.11041238137998
2.34-2.520.10431420.10451256139899
2.52-2.770.12061360.1161243137999
2.77-3.170.15361410.147112581399100
3.17-3.990.14861440.15612421386100
3.99-32.070.13141440.12481237138198

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