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

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Basic information

Entry
Database: PDB / ID: 9ncs
TitleRNase A in complex with Uridine Vanadate and decavanadates
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / 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
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
DECAVANADATE / URIDINE / oxovanadium(2+) / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsGutierrez, C.S. / Lim, D.C. / Silkenath, B. / Kojasoy, V. / Raines, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA073808 United States
CitationJournal: 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
DepositionFeb 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5578
Polymers27,4172
Non-polymers4,1416
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-363-

HOH

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Components

#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 interestY
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 30, 2024 / Details: Varimax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→36.16 Å / Num. obs: 19255 / % possible obs: 33.9 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.064 / Net I/σ(I): 7.62
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.83-1.940.1028340.970.1451
1.94-2.070.06111880.980.0861
2.07-2.240.04511030.9940.0631
2.24-2.450.0389980.9940.0531
2.45-2.740.0348630.9930.0481
2.74-3.160.0517430.9880.0721
3.16-3.860.0246400.9980.0341
3.86-5.430.03750810.0531
5.43-36.160.0462550.9920.0641

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2092 3618 9.96 %
Rwork0.1774 --
obs0.1806 19255 89.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→36.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 171 204 2247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062282
X-RAY DIFFRACTIONf_angle_d0.8773831
X-RAY DIFFRACTIONf_dihedral_angle_d11.031797
X-RAY DIFFRACTIONf_chiral_restr0.049289
X-RAY DIFFRACTIONf_plane_restr0.008338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.850.4999670.5273607X-RAY DIFFRACTION44
1.85-1.880.6088950.4405880X-RAY DIFFRACTION62
1.88-1.910.40881030.3581000X-RAY DIFFRACTION70
1.91-1.930.32351200.30091214X-RAY DIFFRACTION85
1.93-1.960.31151410.26721240X-RAY DIFFRACTION92
1.96-20.23571320.2291306X-RAY DIFFRACTION91
2-2.030.27511530.22031316X-RAY DIFFRACTION93
2.03-2.070.26821440.21561269X-RAY DIFFRACTION92
2.07-2.110.28321460.21321283X-RAY DIFFRACTION92
2.11-2.150.25561370.221278X-RAY DIFFRACTION92
2.15-2.20.2041520.15961357X-RAY DIFFRACTION94
2.2-2.250.21811560.17511257X-RAY DIFFRACTION93
2.25-2.310.23081440.1611274X-RAY DIFFRACTION93
2.31-2.370.20721350.15621340X-RAY DIFFRACTION94
2.37-2.440.17171500.16391309X-RAY DIFFRACTION94
2.44-2.520.21191510.16061357X-RAY DIFFRACTION95
2.52-2.610.18281430.16891299X-RAY DIFFRACTION95
2.61-2.710.24341500.16951368X-RAY DIFFRACTION95
2.71-2.830.19351310.17351287X-RAY DIFFRACTION95
2.83-2.980.18651580.1781372X-RAY DIFFRACTION96
2.98-3.170.21691390.16951337X-RAY DIFFRACTION96
3.17-3.410.1921590.1521321X-RAY DIFFRACTION96
3.41-3.760.17571560.1451373X-RAY DIFFRACTION97
3.76-4.30.16831440.13921344X-RAY DIFFRACTION97
4.3-5.410.14681620.14421379X-RAY DIFFRACTION98
5.42-36.160.21011500.19531355X-RAY DIFFRACTION97
Refinement TLS params.

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

IDL11 (°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)
14.1594-0.9998-2.96162.52961.46566.6012-0.08560.6412-0.3131-0.149-0.06750.1490.2442-0.05220.11230.1644-0.0066-0.02160.2566-0.04040.1099-13.4672-7.647125.0828
27.73191.4721-2.63012.0173-1.32225.57510.0130.4330.3168-0.315-0.0129-0.2380.11380.1356-0.02210.10380.02360.01120.1774-0.01430.1494-9.4686-5.183725.0268
36.87142.04372.7655.53410.98925.4146-0.1071-0.02810.0560.19470.0106-0.2495-0.04250.06870.10360.13180.03520.01430.1039-0.00910.1395-12.378-7.630144.1609
42.27520.2705-0.93821.1431-0.40033.804-0.01320.2685-0.0972-0.1658-0.0976-0.22720.15060.21110.10460.13530.01620.01250.1382-0.00920.1714-7.5993-9.149332.3876
54.0005-2.12143.16454.1475-1.28944.73540.13510.3288-0.0694-0.2307-0.03460.25060.37040.0425-0.10270.184-0.0284-0.02480.1777-0.02080.1077-33.5482-11.30333.2763
62.1810.55870.60480.99240.60442.3952-0.09080.08830.1234-0.05430.03550.1147-0.07540.06490.06790.1331-0.00510.00010.0803-0.00230.1333-30.4946-6.325913.3185
74.60294.6582-4.51016.2787-5.4134.87960.1668-0.58110.60340.5669-0.0180.29040.0286-0.3257-0.10420.26950.06990.05960.23730.03840.3307-37.0436-5.837812.3856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 124 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 42 )
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 124 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 1 )

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