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- PDB-8db6: Adenosine/guanosine nucleoside hydrolase -

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Basic information

Entry
Database: PDB / ID: 8db6
TitleAdenosine/guanosine nucleoside hydrolase
ComponentsInosine-uridine preferring nucleoside hydrolase family protein
KeywordsHYDROLASE / Nucleoside / Adenosine / Guanosine / Parasitic / Inhibitor
Function / homology: / purine nucleosidase activity / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / purine nucleoside catabolic process / metal ion binding / cytosol / Inosine-uridine preferring nucleoside hydrolase family protein
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsMuellers, S.N. / Allen, K.N. / Stockman, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI128585 United States
CitationJournal: Biochemistry / Year: 2022
Title: Structure-Guided Insight into the Specificity and Mechanism of a Parasitic Nucleoside Hydrolase.
Authors: Muellers, S.N. / Nyitray, M.M. / Reynarowych, N. / Saljanin, E. / Benzie, A.L. / Schoenfeld, A.R. / Stockman, B.J. / Allen, K.N.
History
DepositionJun 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Inosine-uridine preferring nucleoside hydrolase family protein
A: Inosine-uridine preferring nucleoside hydrolase family protein
C: Inosine-uridine preferring nucleoside hydrolase family protein
D: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,34211
Polymers133,9054
Non-polymers4377
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-83 kcal/mol
Surface area44760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.596, 75.115, 85.209
Angle α, β, γ (deg.)76.160, 81.488, 88.145
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Inosine-uridine preferring nucleoside hydrolase family protein


Mass: 33476.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_213720 / Production host: Escherichia coli (E. coli) / References: UniProt: A2EYV3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 25% PEG-3350, and 0.1 M Bis-tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.977 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.02→29.65 Å / Num. obs: 76440 / % possible obs: 96.77 % / Redundancy: 3.6 % / Biso Wilson estimate: 38.81 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.052 / Rrim(I) all: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2.02→2.092 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6752 / CC1/2: 0.707 / Rpim(I) all: 0.369 / Rrim(I) all: 0.717 / % possible all: 85.72

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model

Resolution: 2.02→29.65 Å / SU ML: 0.257 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.1265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2371 2000 2.62 %
Rwork0.2044 74432 -
obs0.2053 76432 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.61 Å2
Refinement stepCycle: LAST / Resolution: 2.02→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9222 0 22 358 9602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00839425
X-RAY DIFFRACTIONf_angle_d0.950712800
X-RAY DIFFRACTIONf_chiral_restr0.05781455
X-RAY DIFFRACTIONf_plane_restr0.00571668
X-RAY DIFFRACTIONf_dihedral_angle_d21.34653436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.32241190.29734431X-RAY DIFFRACTION81.02
2.07-2.130.34471440.27285371X-RAY DIFFRACTION97.51
2.13-2.190.29411440.25295360X-RAY DIFFRACTION97.61
2.19-2.260.27361440.24345351X-RAY DIFFRACTION97.78
2.26-2.340.29591450.23745385X-RAY DIFFRACTION97.86
2.34-2.430.2811440.23885381X-RAY DIFFRACTION97.74
2.43-2.540.30171450.23945381X-RAY DIFFRACTION98.03
2.55-2.680.27521450.24425392X-RAY DIFFRACTION98.16
2.68-2.850.30571440.23585362X-RAY DIFFRACTION97.69
2.85-3.070.25781440.22925394X-RAY DIFFRACTION98.42
3.07-3.370.25021470.21125424X-RAY DIFFRACTION98.51
3.37-3.860.21051450.19215416X-RAY DIFFRACTION98.27
3.86-4.860.18451440.16195351X-RAY DIFFRACTION97.74
4.86-29.650.1991460.17455433X-RAY DIFFRACTION98.8

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