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- PDB-8db9: Adenosine/guanosine nucleoside hydrolase bound to inhibitor -

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Basic information

Entry
Database: PDB / ID: 8db9
TitleAdenosine/guanosine nucleoside hydrolase bound to inhibitor
ComponentsInosine-uridine preferring nucleoside hydrolase family protein
KeywordsHYDROLASE/HYDROLASE inhibitor / Nucleoside / Hydrolase / Adenosine / Guanosine / Parasitic / Inhibitor / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


purine nucleosidase activity / purine nucleoside catabolic process / metal ion binding / cytosol
Similarity search - Function
: / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like
Similarity search - Domain/homology
Chem-R1Y / Inosine-uridine preferring nucleoside hydrolase family protein
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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
A: Inosine-uridine preferring nucleoside hydrolase family protein
B: 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)134,79511
Polymers133,9054
Non-polymers8907
Water00
1
A: Inosine-uridine preferring nucleoside hydrolase family protein
B: Inosine-uridine preferring nucleoside hydrolase family protein
C: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules

D: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,79511
Polymers133,9054
Non-polymers8907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4890 Å2
ΔGint-49 kcal/mol
Surface area46260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.406, 75.382, 88.856
Angle α, β, γ (deg.)65.466, 80.791, 87.323
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-R1Y / 1-beta-D-ribofuranosyl-1H-1,2,4-triazole-3-carboximidamide


Mass: 243.220 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.25 Å3/Da / Density % sol: 45.26 %
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: SSRL / Beamline: BL12-2 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.89→38.13 Å / Num. obs: 23552 / % possible obs: 87.89 % / Redundancy: 4.2 % / Biso Wilson estimate: 61.28 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.105 / Rrim(I) all: 0.22 / Net I/σ(I): 6.9
Reflection shellResolution: 2.89→2.993 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2425 / CC1/2: 0.408 / Rpim(I) all: 0.738 / Rrim(I) all: 0.149 / % possible all: 88.09

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Processing

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

Resolution: 2.89→38.13 Å / SU ML: 0.587 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 39.3732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3411 1358 5.87 %
Rwork0.2604 21787 -
obs0.265 23145 88.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.8 Å2
Refinement stepCycle: LAST / Resolution: 2.89→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 55 0 9407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01059600
X-RAY DIFFRACTIONf_angle_d1.252713053
X-RAY DIFFRACTIONf_chiral_restr0.07081484
X-RAY DIFFRACTIONf_plane_restr0.00671705
X-RAY DIFFRACTIONf_dihedral_angle_d23.22693498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.990.41751300.34592207X-RAY DIFFRACTION88.09
2.99-3.110.41551400.34782111X-RAY DIFFRACTION87.08
3.11-3.250.38181350.32382203X-RAY DIFFRACTION88.69
3.25-3.430.39321300.33882099X-RAY DIFFRACTION84.08
3.43-3.640.44991330.33452168X-RAY DIFFRACTION87.79
3.64-3.920.39851340.30892111X-RAY DIFFRACTION85.3
3.92-4.320.35021340.24792162X-RAY DIFFRACTION87.77
4.32-4.940.28281410.21632267X-RAY DIFFRACTION90.73
4.94-6.220.3421380.24532220X-RAY DIFFRACTION90.17
6.22-38.130.24111430.17322239X-RAY DIFFRACTION90.78

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