PDB-9ncs: RNase A in complex with Uridine Vanadate and decavanadates

ID or keywords:

Entry

Database: PDB / ID: 9ncs

Title

RNase A in complex with Uridine Vanadate and decavanadates

Components

Ribonuclease pancreatic

Keywords

HYDROLASE / Ribonuclease / RNA / Uridine Vanadate / decavanadate

Function / homology

Function and homology information

pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.83 Å

Authors

Gutierrez, C.S. / Lim, D.C. / Silkenath, B. / Kojasoy, V. / Raines, R.T.

Funding support

United States, 1items

Citation

Journal: Rna / Year: 2025
Title: Pseudouridine Residues as Substrates for Serum Ribonucleases.
Authors: Gutierrez, C.S. / Silkenath, B. / Kojasoy, V. / Pich, J.A. / Lim, D.C. / Raines, R.T.

History

Deposition	Feb 17, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ncs.cif.gz	159.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9ncs.ent.gz	128.8 KB	Display	PDB format
PDBx/mmJSON format	9ncs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ncs_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	9ncs_full_validation.pdf.gz	3 MB	Display
Data in XML	9ncs_validation.xml.gz	16 KB	Display
Data in CIF	9ncs_validation.cif.gz	21.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nc/9ncs ftp://data.pdbj.org/pub/pdb/validation_reports/nc/9ncs	HTTPS FTP

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Related structure data

Related structure data	9o4vC 9o5bC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#105 - Sep 2008 Ribonuclease A similarity (9) #143 - Nov 2011 Toll-like Receptors similarity (9)

Deposited unit

A: Ribonuclease pancreatic

B: Ribonuclease pancreatic

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	100.053, 32.677, 72.327
Angle α, β, γ (deg.)	90.00, 90.36, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-363- HOH

#1: Protein	Ribonuclease pancreatic / RNase 1 / RNase A Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Pancreas / Plasmid details: Millipore Sigma R6513 / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical	ChemComp-DVT / DECAVANADATE Mass: 957.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O₂₈V₁₀
#3: Chemical	ChemComp-URI / URIDINE Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₂N₂O₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-VVO / oxovanadium(2+) Mass: 66.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OV
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 42.96 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystallization: 50mM Imidazole pH 5.5, 20% PEG 4000 seeded with crystals grown in 20mM Sodium Citrate pH 5.5, 20% PEG 4000 Ligand soaking: 25mM Imidazole pH 5.5, 25% PEG 4000, 7.5mM Uridine Vanadate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 30, 2024 / Details: Varimax HF

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.83→36.16 Å / Num. obs: 19255 / % possible obs: 33.9 % / Redundancy: 3.6 % / CC_1/2: 0.996 / R_merge(I) obs: 0.046 / R_rim(I) all: 0.064 / Net I/σ(I): 7.62

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.83-1.94	0.102	834	0.97	0.145	1
1.94-2.07	0.061	1188	0.98	0.086	1
2.07-2.24	0.045	1103	0.994	0.063	1
2.24-2.45	0.038	998	0.994	0.053	1
2.45-2.74	0.034	863	0.993	0.048	1
2.74-3.16	0.051	743	0.988	0.072	1
3.16-3.86	0.024	640	0.998	0.034	1
3.86-5.43	0.037	508	1	0.053	1
5.43-36.16	0.046	255	0.992	0.064	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.83→36.16 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2092	3618	9.96 %
R_work	0.1774	-	-
obs	0.1806	19255	89.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.83→36.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1872	0	171	204	2247

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2282
X-RAY DIFFRACTION	f_angle_d	0.877	3831
X-RAY DIFFRACTION	f_dihedral_angle_d	11.031	797
X-RAY DIFFRACTION	f_chiral_restr	0.049	289
X-RAY DIFFRACTION	f_plane_restr	0.008	338

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 (%)
1.83-1.85	0.4999	67	0.5273	607	X-RAY DIFFRACTION	44
1.85-1.88	0.6088	95	0.4405	880	X-RAY DIFFRACTION	62
1.88-1.91	0.4088	103	0.358	1000	X-RAY DIFFRACTION	70
1.91-1.93	0.3235	120	0.3009	1214	X-RAY DIFFRACTION	85
1.93-1.96	0.3115	141	0.2672	1240	X-RAY DIFFRACTION	92
1.96-2	0.2357	132	0.229	1306	X-RAY DIFFRACTION	91
2-2.03	0.2751	153	0.2203	1316	X-RAY DIFFRACTION	93
2.03-2.07	0.2682	144	0.2156	1269	X-RAY DIFFRACTION	92
2.07-2.11	0.2832	146	0.2132	1283	X-RAY DIFFRACTION	92
2.11-2.15	0.2556	137	0.22	1278	X-RAY DIFFRACTION	92
2.15-2.2	0.204	152	0.1596	1357	X-RAY DIFFRACTION	94
2.2-2.25	0.2181	156	0.1751	1257	X-RAY DIFFRACTION	93
2.25-2.31	0.2308	144	0.161	1274	X-RAY DIFFRACTION	93
2.31-2.37	0.2072	135	0.1562	1340	X-RAY DIFFRACTION	94
2.37-2.44	0.1717	150	0.1639	1309	X-RAY DIFFRACTION	94
2.44-2.52	0.2119	151	0.1606	1357	X-RAY DIFFRACTION	95
2.52-2.61	0.1828	143	0.1689	1299	X-RAY DIFFRACTION	95
2.61-2.71	0.2434	150	0.1695	1368	X-RAY DIFFRACTION	95
2.71-2.83	0.1935	131	0.1735	1287	X-RAY DIFFRACTION	95
2.83-2.98	0.1865	158	0.178	1372	X-RAY DIFFRACTION	96
2.98-3.17	0.2169	139	0.1695	1337	X-RAY DIFFRACTION	96
3.17-3.41	0.192	159	0.152	1321	X-RAY DIFFRACTION	96
3.41-3.76	0.1757	156	0.145	1373	X-RAY DIFFRACTION	97
3.76-4.3	0.1683	144	0.1392	1344	X-RAY DIFFRACTION	97
4.3-5.41	0.1468	162	0.1442	1379	X-RAY DIFFRACTION	98
5.42-36.16	0.2101	150	0.1953	1355	X-RAY DIFFRACTION	97

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.1594	-0.9998	-2.9616	2.5296	1.4656	6.6012	-0.0856	0.6412	-0.3131	-0.149	-0.0675	0.149	0.2442	-0.0522	0.1123	0.1644	-0.0066	-0.0216	0.2566	-0.0404	0.1099	-13.4672	-7.6471	25.0828
2	7.7319	1.4721	-2.6301	2.0173	-1.3222	5.5751	0.013	0.433	0.3168	-0.315	-0.0129	-0.238	0.1138	0.1356	-0.0221	0.1038	0.0236	0.0112	0.1774	-0.0143	0.1494	-9.4686	-5.1837	25.0268
3	6.8714	2.0437	2.765	5.5341	0.9892	5.4146	-0.1071	-0.0281	0.056	0.1947	0.0106	-0.2495	-0.0425	0.0687	0.1036	0.1318	0.0352	0.0143	0.1039	-0.0091	0.1395	-12.378	-7.6301	44.1609
4	2.2752	0.2705	-0.9382	1.1431	-0.4003	3.804	-0.0132	0.2685	-0.0972	-0.1658	-0.0976	-0.2272	0.1506	0.2111	0.1046	0.1353	0.0162	0.0125	0.1382	-0.0092	0.1714	-7.5993	-9.1493	32.3876
5	4.0005	-2.1214	3.1645	4.1475	-1.2894	4.7354	0.1351	0.3288	-0.0694	-0.2307	-0.0346	0.2506	0.3704	0.0425	-0.1027	0.184	-0.0284	-0.0248	0.1777	-0.0208	0.1077	-33.5482	-11.3033	3.2763
6	2.181	0.5587	0.6048	0.9924	0.6044	2.3952	-0.0908	0.0883	0.1234	-0.0543	0.0355	0.1147	-0.0754	0.0649	0.0679	0.1331	-0.0051	0.0001	0.0803	-0.0023	0.1333	-30.4946	-6.3259	13.3185
7	4.6029	4.6582	-4.5101	6.2787	-5.413	4.8796	0.1668	-0.5811	0.6034	0.5669	-0.018	0.2904	0.0286	-0.3257	-0.1042	0.2695	0.0699	0.0596	0.2373	0.0384	0.3307	-37.0436	-5.8378	12.3856

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 50 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 51 through 71 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 72 through 124 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 42 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 43 through 124 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 1 )

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