PDB-9oks: 16mer self-complementary duplex RNA with dA:U pair sequence 1

ID or keywords:

Entry

Database: PDB / ID: 9oks

Title

16mer self-complementary duplex RNA with dA:U pair sequence 1

Components

DNA/RNA (5'-R(*AP*GP*AP*G)-D(P*A)-R(P*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3')

Keywords

RNA / Deoxyribo-purine / RNA duplex / Origin of Life

Function / homology

DNA/RNA hybrid / DNA/RNA hybrid (> 10)

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Fang, Z. / Szostak, J.W.

Funding support

United States, 2items

Citation

Journal: Biorxiv / Year: 2025
Title: Impact of 2'-deoxyribo-purine substrates on nonenzymatic RNA template-directed primer extension.
Authors: Fang, Z. / Acikgoz, O. / Jia, X. / Essex, J. / Wen, R. / Szostak, J.W.

History

Deposition	May 11, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9oks.cif.gz	25.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9oks.ent.gz	13.9 KB	Display	PDB format
PDBx/mmJSON format	9oks.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9oks_validation.pdf.gz	363.9 KB	Display	wwPDB validaton report
Full document	9oks_full_validation.pdf.gz	364.1 KB	Display
Data in XML	9oks_validation.xml.gz	3.8 KB	Display
Data in CIF	9oks_validation.cif.gz	5.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ok/9oks ftp://data.pdbj.org/pub/pdb/validation_reports/ok/9oks	HTTPS FTP

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Related structure data

Related structure data	9oktC 9okuC 9okvC 9okwC 9okxC 9okyC 9okzC 9ol0C 9ol1C 9ol2C 9ol3C C: citing same article (ref.)
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	#130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: DNA/RNA (5'-R(*AP*GP*AP*G)-D(P*A)-R(P*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3')

hetero molecules

5.12 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA/RNA (5'-R(*AP*GP*AP*G)-D(P*A)-R(P*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3')

hetero molecules

A: DNA/RNA (5'-R(*AP*GP*AP*G)-D(P*A)-R(P*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3')

hetero molecules

defined by author&software
10.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	41.204, 41.204, 125.586
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-241- HOH
2	1	A-242- HOH
3	1	A-251- HOH
4	1	A-260- HOH
5	1	A-282- HOH

#1: DNA/RNA hybrid	DNA/RNA (5'-R(APGPAPG)-D(PA)-R(PAPGPAPUPCPUPUPCPUPCPU)-3') Mass: 5067.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.02 Å³/Da / Density % sol: 39.05 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.08 M Sodium chloride, 0.012 M Potassium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 6.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

Diffraction	Mean temperature: 99 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 30, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97741 Å / Relative weight: 1
Reflection	Resolution: 1.5→50 Å / Num. obs: 6909 / % possible obs: 100 % / Redundancy: 8.7 % / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.024 / R_rim(I) all: 0.071 / Χ²: 0.978 / Net I/σ(I): 30
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 8.2 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 4 / Num. unique obs: 334 / CC_1/2: 0.919 / CC star: 0.979 / R_pim(I) all: 0.186 / R_rim(I) all: 0.544 / Χ²: 0.953 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→41.862 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.955 / SU B: 1.31 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2099	341	5.057 %
R_work	0.1661	6402	-
all	0.168	-	-
obs	-	6743	97.583 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 10.313 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.001 Å²	-0 Å²	-0 Å²
2-	-	-0.001 Å²	-0 Å²
3-	-	-	0.003 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→41.862 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	335	2	88	425

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.011	374
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.018	156
X-RAY DIFFRACTION	r_angle_refined_deg	2.01	1.837	580
X-RAY DIFFRACTION	r_angle_other_deg	0.648	1.643	381
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.072	5	11
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	78
X-RAY DIFFRACTION	r_gen_planes_refined	0.029	0.02	185
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	59
X-RAY DIFFRACTION	r_nbd_refined	0.091	0.2	28
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	154
X-RAY DIFFRACTION	r_nbtor_refined	0.25	0.2	136
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	94
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	47
X-RAY DIFFRACTION	r_metal_ion_refined	0.056	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.109	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.124	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.163	0.2	33
X-RAY DIFFRACTION	r_scbond_it	1.188	1.121	374
X-RAY DIFFRACTION	r_scbond_other	1.187	1.12	375
X-RAY DIFFRACTION	r_scangle_it	1.745	2.052	580
X-RAY DIFFRACTION	r_scangle_other	1.743	2.051	581
X-RAY DIFFRACTION	r_lrange_it	5.57	20.841	526
X-RAY DIFFRACTION	r_lrange_other	5.045	15.539	502

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.5-1.539	0.238	12	0.198	362	0.199	499	0.956	0.974	74.9499	0.173
1.539-1.581	0.182	19	0.179	445	0.179	499	0.975	0.98	92.986	0.157
1.581-1.626	0.299	22	0.195	429	0.2	455	0.955	0.974	99.1209	0.166
1.626-1.676	0.224	25	0.173	440	0.176	466	0.97	0.982	99.7854	0.15
1.676-1.731	0.198	17	0.177	429	0.178	446	0.981	0.98	100	0.155
1.731-1.792	0.234	21	0.169	417	0.172	438	0.965	0.981	100	0.152
1.792-1.859	0.263	22	0.174	394	0.178	416	0.945	0.981	100	0.16
1.859-1.935	0.173	20	0.171	382	0.171	402	0.984	0.981	100	0.153
1.935-2.021	0.251	11	0.156	371	0.159	382	0.963	0.985	100	0.15
2.021-2.119	0.164	23	0.153	356	0.154	379	0.983	0.985	100	0.144
2.119-2.234	0.237	18	0.183	334	0.186	352	0.98	0.981	100	0.18
2.234-2.369	0.225	19	0.175	317	0.178	336	0.975	0.983	100	0.18
2.369-2.532	0.227	24	0.173	301	0.177	325	0.971	0.983	100	0.177
2.532-2.734	0.288	15	0.196	287	0.2	302	0.955	0.978	100	0.212
2.734-2.994	0.257	17	0.157	260	0.162	277	0.97	0.984	100	0.177
2.994-3.345	0.14	12	0.135	236	0.135	249	0.995	0.991	99.5984	0.176
3.345-3.858	0.244	18	0.145	206	0.151	225	0.958	0.989	99.5556	0.19
3.858-4.715	0.203	10	0.156	188	0.157	198	0.975	0.988	100	0.206
4.715-6.626	0.188	9	0.161	150	0.163	159	0.992	0.985	100	0.223
6.626-41.862	0.111	7	0.169	98	0.164	105	0.994	0.987	100	0.249

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