[English] 日本語
Yorodumi
- PDB-8rih: Crystal structure of the Saccharomyces cerevisiae URH1p riboside ... -

+
Open data


ID or keywords:

Loading...

-
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 / homology
Function and homology information


uridine nucleosidase activity / purine nucleosidase activity / purine nucleoside catabolic process / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Uridine ribohydrolase
Similarity search - Component
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more