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- PDB-6jr4: Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster -

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Basic information

Entry
Database: PDB / ID: 6jr4
TitleCrystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster
ComponentsDNA (5'-D(*CP*AP*CP*CP*TP*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 / SAD / Resolution: 1.798 Å
AuthorsKondo, J. / Cerretani, C. / Kanazawa, H. / Vosch, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H03033 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Crystal structure of a NIR-Emitting DNA-Stabilized Ag16Nanocluster.
Authors: Cerretani, C. / Kanazawa, H. / Vosch, T. / Kondo, J.
History
DepositionApr 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 25, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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


Theoretical massNumber of molelcules
Total (without water)16,23544
Polymers12,0564
Non-polymers4,17940
Water1,08160
1
A: DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3')
B: DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,11822
Polymers6,0282
Non-polymers2,09020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-134 kcal/mol
Surface area2590 Å2
MethodPISA
2
C: DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3')
D: DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,11822
Polymers6,0282
Non-polymers2,09020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-136 kcal/mol
Surface area2590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.241, 33.849, 58.863
Angle α, β, γ (deg.)90.000, 97.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3013.995 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.: 38 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAg Atom: A101-A113, B101-B105, C101-C113, and D101-D105, Ag Ion: B106 and D106

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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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MOPS, PEG3350, Spermine, calcium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 2 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.798→24.016 Å / Num. obs: 16247 / % possible obs: 94.3 % / Redundancy: 3.224 % / Biso Wilson estimate: 6.46 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.1 / Χ2: 1.591 / Net I/σ(I): 10.85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.852.970.1535.4510560.970.18583.1
1.85-1.92.9770.1315.9311150.9740.15989.3
1.9-1.952.8150.2045.6610340.9410.25287.6
1.95-2.013.2060.1117.9911060.9790.13392.4
2.01-2.083.2290.0899.5710570.9870.10793
2.08-2.153.2070.09110.6110240.9840.10994.8
2.15-2.233.1610.08210.6310280.9920.09894.4
2.23-2.322.870.09111.079460.9790.11293
2.32-2.433.3180.07312.949820.9910.08796.6
2.43-2.543.4480.07414.018580.9890.08797.1
2.54-2.683.4630.07813.968920.9890.09198
2.68-2.843.4250.07413.268070.990.08898.5
2.84-3.043.3720.0812.48060.9880.09699.4
3.04-3.283.2790.0812.517310.990.095100
3.28-3.63.0990.07412.136640.9920.0998.8
3.6-4.023.1970.08213.196130.9890.09998.9
4.02-4.643.7160.07714.525450.990.09100
4.64-5.693.6980.0715.434400.9920.08199.8
5.69-8.043.6770.0716.43650.9910.08299.7
8.04-24.0163.4620.07716.811710.9860.09491

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.798→24.016 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.92
RfactorNum. reflection% reflection
Rfree0.146 1644 10.12 %
Rwork0.1263 --
obs0.1282 16247 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.63 Å2 / Biso mean: 20.45 Å2 / Biso min: 10.01 Å2
Refinement stepCycle: final / Resolution: 1.798→24.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 800 40 60 900
Biso mean--13.78 23.45 -
Num. residues----40
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007896
X-RAY DIFFRACTIONf_angle_d1.1221372
X-RAY DIFFRACTIONf_chiral_restr0.067156
X-RAY DIFFRACTIONf_plane_restr0.00940
X-RAY DIFFRACTIONf_dihedral_angle_d30.734384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7978-1.85070.15531240.14951054117882
1.8507-1.91040.19441260.16211176130289
1.9104-1.97860.17811300.15881160129090
1.9786-2.05780.13991280.11211185131393
2.0578-2.15140.12731420.10221201134394
2.1514-2.26480.16331310.12321229136093
2.2648-2.40650.1121420.09421238138096
2.4065-2.59210.10671350.08921261139697
2.5921-2.85260.11071420.11611252139498
2.8526-3.26450.16381610.151912841445100
3.2645-4.10960.20031470.17741273142099
4.1096-24.01830.14281360.13041290142699

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