PDB-9khw: A DNA-stabilized atomically precise silver nanorod with emission ...

ID or keywords:

Entry

Database: PDB / ID: 9khw

Title

A DNA-stabilized atomically precise silver nanorod with emission at 960 nm

Components

DNA (5'-D(*CP*CP*GP*CP*GP*CP*GP*CP*GP*CP*CP*GP*CP*GP*AP*A)-3')

Keywords

DNA / silver / Ag28 / near infrared emission / fluorescence / DNA-AgNC

Function / homology

SILVER ION / DNA / DNA (> 10)

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.3 Å

Authors

Kanazawa, H. / Kondo, J. / Romolini, G. / Cerretani, C. / Lanza, A. / Huang, Z. / Vosch, T.

Funding support

Denmark, European Union,

Japan, 5items

Organization	Grant number	Country
Novo Nordisk Foundation	NNF22OC0073734	Denmark
Independent Research Fund Denmark - Technology and Production Sciences	0136-00024B	Denmark
Independent Research Fund Denmark - Technology and Production Sciences	3103-00279B	Denmark
Marie Sklodowska-Curie Actions, FragNET ITN	NIR-emitting Ag-DNAs 101151897	European Union
Japan Agency for Medical Research and Development (AMED)	JP24ama121014	Japan

Citation

Journal: Small Struct / Year: 2025
Title: Shining Bright at 960 nm: A 28-Silver-Atom Nanorod Stabilized by DNA
Authors: Romolini, G. / Kanazawa, H. / Mollerup, C. / Lisberg, M. / Lind, S. / Huang, Z. / Cerretani, C. / Kondo, J. / Vosch, T.

History

Deposition	Nov 11, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9khw.cif.gz	30.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9khw.ent.gz	19.6 KB	Display	PDB format
PDBx/mmJSON format	9khw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9khw_validation.pdf.gz	23.9 MB	Display	wwPDB validaton report
Full document	9khw_full_validation.pdf.gz	23.9 MB	Display
Data in XML	9khw_validation.xml.gz	3.9 KB	Display
Data in CIF	9khw_validation.cif.gz	5.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kh/9khw ftp://data.pdbj.org/pub/pdb/validation_reports/kh/9khw	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#255 - Mar 2021 Cisplatin and DNA similarity (2) #67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #23 - Nov 2001 DNA similarity (2) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

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NCBI

Related items in Molecule of the Month

#255 - Mar 2021
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similarity (1)
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#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
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similarity (1)
#160 - Apr 2013
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similarity (1)
#190 - Oct 2015
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#240 - Dec 2019
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similarity (1)
#257 - May 2021
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similarity (1)
#258 - Jun 2021
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similarity (1)
#31 - Jul 2002
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similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
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similarity (1)
#55 - Jul 2004
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#7 - Jul 2000
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Deposited unit

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

B: DNA (5'-D(*CP*CP*GP*CP*GP*CP*GP*CP*GP*CP*CP*GP*CP*GP*AP*A)-3')

hetero molecules

12.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry, Electron Dispersive X-ray Spectroscopy

Unit cell

Length a, b, c (Å)	27.215, 53.171, 27.215
Angle α, β, γ (deg.)	90.00, 103.67, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: DNA chain	DNA (5'-D(CPCPGPCPGPCPGPCPGPCPCPGPCPGPAPA)-3') Mass: 4870.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical	... ChemComp-AG / SILVER ION Mass: 107.868 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	1.96	37.38
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
293	1	vapor diffusion, sitting drop	7	50 mM MOPS, 10 mM spermine, 10 mM KNO3, 10% MPD
293	2	vapor diffusion, hanging drop	7	50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Ca(NO3), 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol.

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	Y
2	100	2	Y

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	Photon Factory	BL-5A	1	1.9
SYNCHROTRON	MAX IV	BioMAX	2	0.6199

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M	1	PIXEL	Oct 12, 2024
DECTRIS EIGER2 S 16M	2	PIXEL	Oct 20, 2024

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.9	1
2	0.6199	1

Reflection

Resolution: 1.3→26.4 Å / Num. obs: 35689 / % possible obs: 97.1 % / Redundancy: 3.6 % / CC_1/2: 0.993 / R_merge(I) obs: 0.111 / R_rim(I) all: 0.13 / Net I/σ(I): 7.25

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.3-1.33	0.319	2549	0.899	0.376	2
1.33-1.37	0.288	2543	0.918	0.339	2
1.37-1.41	0.266	2478	0.939	0.314	2
1.41-1.45	0.267	2443	0.933	0.315	2
1.45-1.5	0.247	2414	0.938	0.291	2
1.5-1.55	0.249	2202	0.931	0.295	2
1.55-1.61	0.235	2257	0.951	0.275	2
1.61-1.67	0.203	2089	0.96	0.238	2
1.67-1.75	0.184	2071	0.962	0.216	2
1.75-1.83	0.154	1967	0.973	0.181	2
1.83-1.93	0.133	1919	0.982	0.156	2
1.93-2.05	0.102	1737	0.987	0.12	2
2.05-2.19	0.089	1646	0.989	0.104	2
2.19-2.37	0.074	1539	0.992	0.087	2
2.37-2.59	0.068	1371	0.996	0.08	2
2.59-2.9	0.076	1268	0.991	0.089	2
2.9-3.35	0.068	1143	0.995	0.079	2
3.35-4.1	0.067	939	0.995	0.077	2
4.1-5.8	0.063	742	0.994	0.074	2
5.8-26.4	0.056	372	0.995	0.065	2
2-26.6		9236	0.994		1

Serial crystallography sample delivery

ID	Method
1	fixed target
2	fixed target

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XSCALE		data scaling
Sir2014	Sir2019	phasing
AutoSol		phasing
XDS		data reduction

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.3→16.82 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1642	3521	9.88 %
R_work	0.1631	-	-
obs	0.1632	35654	97.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.3→16.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	646	30	39	715

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	724
X-RAY DIFFRACTION	f_angle_d	1.21	1112
X-RAY DIFFRACTION	f_dihedral_angle_d	28.714	312
X-RAY DIFFRACTION	f_chiral_restr	0.097	126
X-RAY DIFFRACTION	f_plane_restr	0.018	32

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.3-1.31	0.2676	132	0.2335	1189	X-RAY DIFFRACTION	96
1.31-1.33	0.2502	138	0.2342	1257	X-RAY DIFFRACTION	96
1.33-1.35	0.2243	146	0.2214	1303	X-RAY DIFFRACTION	97
1.35-1.37	0.2757	143	0.2155	1280	X-RAY DIFFRACTION	96
1.37-1.4	0.2001	139	0.2181	1244	X-RAY DIFFRACTION	96
1.4-1.42	0.18	142	0.2176	1318	X-RAY DIFFRACTION	98
1.42-1.45	0.1995	136	0.2127	1272	X-RAY DIFFRACTION	97
1.45-1.47	0.1992	147	0.2026	1337	X-RAY DIFFRACTION	98
1.47-1.5	0.1946	143	0.2146	1276	X-RAY DIFFRACTION	97
1.5-1.54	0.2174	147	0.2155	1256	X-RAY DIFFRACTION	97
1.54-1.57	0.2367	140	0.1921	1311	X-RAY DIFFRACTION	97
1.57-1.61	0.2775	142	0.211	1291	X-RAY DIFFRACTION	98
1.61-1.66	0.2026	139	0.1801	1287	X-RAY DIFFRACTION	98
1.66-1.7	0.1607	148	0.1841	1335	X-RAY DIFFRACTION	98
1.7-1.76	0.1409	141	0.1702	1258	X-RAY DIFFRACTION	98
1.76-1.82	0.1497	145	0.1652	1323	X-RAY DIFFRACTION	98
1.82-1.89	0.1351	136	0.1396	1283	X-RAY DIFFRACTION	98
1.89-1.98	0.1499	145	0.1281	1309	X-RAY DIFFRACTION	98
1.98-2.08	0.1304	137	0.1284	1310	X-RAY DIFFRACTION	98
2.09-2.21	0.1258	125	0.1232	1313	X-RAY DIFFRACTION	98
2.21-2.39	0.1093	144	0.1226	1294	X-RAY DIFFRACTION	97
2.39-2.62	0.1062	149	0.1157	1239	X-RAY DIFFRACTION	96
2.62-3	0.1635	133	0.143	1298	X-RAY DIFFRACTION	97
3-3.78	0.1747	138	0.1657	1302	X-RAY DIFFRACTION	98
3.78-16.82	0.1749	146	0.1688	1248	X-RAY DIFFRACTION	95

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