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- PDB-8qnd: Crystal structure of the ribonucleoside hydrolase C from Lactobac... -

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Basic information

Entry
Database: PDB / ID: 8qnd
TitleCrystal structure of the ribonucleoside hydrolase C from Lactobacillus reuteri
ComponentsInosine-uridine nucleoside N-ribohydrolase
KeywordsHYDROLASE / Ribonucleoside hydrolase C / lactobacilli
Function / homology
Function and homology information


purine nucleosidase activity / purine nucleoside catabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / metal ion binding / cytosol
Similarity search - Function
Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like
Similarity search - Domain/homology
Inosine-uridine nucleoside N-ribohydrolase
Similarity search - Component
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMatyuta, I.O. / Minyaev, M.E. / Shaposhnikov, L.A. / Pometun, A.A. / Tishkov, V.I. / Popov, V.O. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-64-10029 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structure-Functional Examination of Novel Ribonucleoside Hydrolase C (RihC) from Limosilactobacillus reuteri LR1.
Authors: Shaposhnikov, L.A. / Chikurova, N.Y. / Atroshenko, D.L. / Savin, S.S. / Kleymenov, S.Y. / Chernobrovkina, A.V. / Pometun, E.V. / Minyaev, M.E. / Matyuta, I.O. / Hushpulian, D.M. / Boyko, K.M. ...Authors: Shaposhnikov, L.A. / Chikurova, N.Y. / Atroshenko, D.L. / Savin, S.S. / Kleymenov, S.Y. / Chernobrovkina, A.V. / Pometun, E.V. / Minyaev, M.E. / Matyuta, I.O. / Hushpulian, D.M. / Boyko, K.M. / Tishkov, V.I. / Pometun, A.A.
History
DepositionSep 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 16, 2024Group: Structure summary / Category: audit_author / pdbx_entry_details
Item: _audit_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine-uridine nucleoside N-ribohydrolase
B: Inosine-uridine nucleoside N-ribohydrolase
C: Inosine-uridine nucleoside N-ribohydrolase
D: Inosine-uridine nucleoside N-ribohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,92010
Polymers133,6794
Non-polymers2406
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-111 kcal/mol
Surface area42290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.112, 81.530, 86.847
Angle α, β, γ (deg.)90.00, 95.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Inosine-uridine nucleoside N-ribohydrolase


Mass: 33419.824 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus reuteri (bacteria) / Gene: rihC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5JJT3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→63.38 Å / Num. obs: 91739 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.914 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.039 / Rrim(I) all: 0.091 / Χ2: 1.03 / Net I/σ(I): 19.5 / Num. measured all: 585566
Reflection shellResolution: 1.9→1.93 Å / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.347 / Num. measured all: 29786 / Num. unique obs: 4547 / CC1/2: 0.956 / Rpim(I) all: 0.146 / Rrim(I) all: 0.377 / Χ2: 1 / Net I/σ(I) obs: 5.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→63.38 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.871 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20077 4557 5 %RANDOM
Rwork0.1684 ---
obs0.16996 87159 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.401 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å20.62 Å2
2---0.26 Å20 Å2
3---1.49 Å2
Refinement stepCycle: 1 / Resolution: 1.9→63.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8847 0 6 766 9619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0139073
X-RAY DIFFRACTIONr_bond_other_d0.0050.0168532
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.63912347
X-RAY DIFFRACTIONr_angle_other_deg1.4731.57819715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47551182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98925.14356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.933151457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2321511
X-RAY DIFFRACTIONr_chiral_restr0.1080.21289
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0210249
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021797
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5912.2574735
X-RAY DIFFRACTIONr_mcbond_other2.5812.2564733
X-RAY DIFFRACTIONr_mcangle_it3.5833.3635902
X-RAY DIFFRACTIONr_mcangle_other3.5853.3645903
X-RAY DIFFRACTIONr_scbond_it3.2012.5224338
X-RAY DIFFRACTIONr_scbond_other3.1992.5224338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5833.6636441
X-RAY DIFFRACTIONr_long_range_B_refined5.70527.2779990
X-RAY DIFFRACTIONr_long_range_B_other5.63826.9989781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A92260.06
12B92260.06
21A92190.07
22C92190.07
31A91740.06
32D91740.06
41B92650.07
42C92650.07
51B90910.07
52D90910.07
61C90990.08
62D90990.08
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 377 -
Rwork0.181 6421 -
obs--99.91 %

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