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- PDB-8rih: Crystal structure of the Saccharomyces cerevisiae URH1p riboside ... -

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Basic information

Entry
Database: PDB / ID: 8rih
TitleCrystal structure of the Saccharomyces cerevisiae URH1p riboside hydrolase
ComponentsUridine ribohydrolase
KeywordsHYDROLASE / Nucleosidase / nucleoside hydrolase / riboside hydrolase
Function / homologyuridine nucleosidase activity / Inosine/uridine-preferring nucleoside hydrolase, conserved site / Inosine-uridine preferring nucleoside hydrolase family signature. / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / nucleobase-containing compound metabolic process / Uridine ribohydrolase
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsDegano, M. / Carriles, A.A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG25764 Italy
CitationJournal: Int J Mol Sci / Year: 2024
Title: Structure-Function Insights into the Dual Role in Nucleobase and Nicotinamide Metabolism and a Possible Use in Cancer Gene Therapy of the URH1p Riboside Hydrolase.
Authors: Carriles, A.A. / Muzzolini, L. / Minici, C. / Tornaghi, P. / Patrone, M. / Degano, M.
History
DepositionDec 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine ribohydrolase
B: Uridine ribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8356
Polymers76,5112
Non-polymers3244
Water75742
1
A: Uridine ribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4183
Polymers38,2551
Non-polymers1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uridine ribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4183
Polymers38,2551
Non-polymers1622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.284, 140.284, 81.343
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 340 / Label seq-ID: 7 - 343

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Uridine ribohydrolase


Mass: 38255.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: URH1, SCY_1288 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6ZZ00
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.05 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM TrisHCl, 800 mM LiCl, 32% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2022 / Details: CRLs, multilayer mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.6→121.49 Å / Num. obs: 13763 / % possible obs: 94.1 % / Redundancy: 12.9 % / CC1/2: 0.981 / Rpim(I) all: 0.167 / Net I/σ(I): 5.9
Reflection shellResolution: 2.6→2.89 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7714 / CC1/2: 0.57 / Rpim(I) all: 0.988 / % possible all: 81.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→121.49 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.881 / SU B: 31.74 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R Free: 0.487
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 714 5.272 %Random selection
Rwork0.1859 12828 --
all0.188 ---
obs-13542 56.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.035 Å20.017 Å20 Å2
2--0.035 Å2-0 Å2
3----0.112 Å2
Refinement stepCycle: LAST / Resolution: 2.74→121.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5220 0 18 42 5280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125389
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165007
X-RAY DIFFRACTIONr_angle_refined_deg0.9081.6547307
X-RAY DIFFRACTIONr_angle_other_deg0.2951.57811573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.505520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06910864
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.93610242
X-RAY DIFFRACTIONr_chiral_restr0.0410.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021205
X-RAY DIFFRACTIONr_nbd_refined0.1990.21200
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.25249
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22729
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2138
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1750.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.140.218
X-RAY DIFFRACTIONr_nbd_other0.1760.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.27
X-RAY DIFFRACTIONr_mcbond_it1.1511.0552662
X-RAY DIFFRACTIONr_mcbond_other1.1491.0552659
X-RAY DIFFRACTIONr_mcangle_it1.972.3663313
X-RAY DIFFRACTIONr_mcangle_other1.972.3663314
X-RAY DIFFRACTIONr_scbond_it1.4491.1852727
X-RAY DIFFRACTIONr_scbond_other1.4491.1862728
X-RAY DIFFRACTIONr_scangle_it2.4562.6653994
X-RAY DIFFRACTIONr_scangle_other2.4562.6663995
X-RAY DIFFRACTIONr_lrange_it4.74310.57723255
X-RAY DIFFRACTIONr_lrange_other4.74310.57723252
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.0511354
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.059460.0501
12AX-RAY DIFFRACTIONLocal ncs0.059460.0501
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.74-2.8110.319100.2922090.29317930.9080.94512.21420.291
2.811-2.8880.298170.282330.28116910.9450.95114.78420.28
2.888-2.9720.422110.262800.26616900.9580.96517.21890.266
2.972-3.0630.308150.2483410.25116430.9280.96321.66770.251
3.063-3.1640.239370.254000.24915870.9590.95927.53620.246
3.164-3.2750.206100.2344730.23315180.9870.96631.81820.226
3.275-3.3980.256350.2295110.23114930.960.96536.57070.221
3.398-3.5370.235330.2075630.20814090.9680.97342.29950.193
3.537-3.6940.261500.2036680.20713990.960.97451.32240.186
3.694-3.8740.248520.2119770.21312830.9650.96980.20270.185
3.874-4.0830.273560.20411750.20712390.9460.9799.35430.183
4.083-4.3310.199660.18411140.18511800.9760.9781000.168
4.331-4.6290.176410.16110710.16111120.9790.9831000.146
4.629-50.188480.1479920.14910400.9780.9861000.138
5-5.4760.215640.1548880.1589520.9730.9861000.147
5.476-6.1210.23500.1848250.1878750.9710.9811000.172
6.121-7.0640.227450.1847230.1867680.9720.981000.174
7.064-8.6450.188280.1546240.1566530.9780.98599.84690.156
8.645-12.1950.174310.1414790.1445100.9820.9871000.157
12.195-121.490.26150.2012810.2042990.9550.97298.99670.27
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)
11.66610.37240.25981.9817-0.47573.5649-0.027-0.0211-0.0688-0.0497-0.04860.18620.3053-0.19330.07560.1404-0.06120.01160.1836-0.0440.223446.404-51.913-0.127
21.53270.42030.22962.2028-0.33935.21640.041-0.1024-0.37850.04390.05050.130.5265-0.4291-0.09150.1761-0.01680.0370.24190.04790.32164.563-66.35737.126
Refinement TLS groupSelection: ALL

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