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- PDB-8db7: Adenosine/guanosine nucleoside hydrolase bound to a fragment inhibitor -

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Basic information

Entry
Database: PDB / ID: 8db7
TitleAdenosine/guanosine nucleoside hydrolase bound to a fragment 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-R2O / Inosine-uridine preferring nucleoside hydrolase family protein
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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)134,97215
Polymers133,9054
Non-polymers1,06611
Water4,270237
1
B: Inosine-uridine preferring nucleoside hydrolase family protein
A: 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)134,97215
Polymers133,9054
Non-polymers1,06611
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6380 Å2
ΔGint-89 kcal/mol
Surface area44320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.651, 74.537, 85.641
Angle α, β, γ (deg.)83.019, 80.897, 89.900
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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-R2O / N-(4-fluorophenyl)-4,5-dihydro-1H-imidazol-2-amine


Mass: 179.194 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H10FN3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
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: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.33→29.99 Å / Num. obs: 51489 / % possible obs: 98.15 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.1 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.073 / Rrim(I) all: 0.19 / Net I/σ(I): 8.6
Reflection shellResolution: 2.33→2.413 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5011 / CC1/2: 0.839 / Rpim(I) all: 0.304 / Rrim(I) all: 0.775 / % possible all: 95.26

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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: 2.33→29.99 Å / SU ML: 0.3539 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.3254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2558 2000 3.88 %
Rwork0.1955 49489 -
obs0.1979 51489 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.41 Å2
Refinement stepCycle: LAST / Resolution: 2.33→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9376 0 61 237 9674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00899627
X-RAY DIFFRACTIONf_angle_d1.057513075
X-RAY DIFFRACTIONf_chiral_restr0.06761474
X-RAY DIFFRACTIONf_plane_restr0.00591709
X-RAY DIFFRACTIONf_dihedral_angle_d22.49383495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.390.36761300.27173195X-RAY DIFFRACTION89.02
2.39-2.450.37681420.26653533X-RAY DIFFRACTION97.82
2.45-2.520.3461450.25423570X-RAY DIFFRACTION98.05
2.52-2.60.32081420.24373533X-RAY DIFFRACTION98.42
2.6-2.70.29711440.23783563X-RAY DIFFRACTION98.43
2.7-2.80.27941450.21943587X-RAY DIFFRACTION98.47
2.8-2.930.29621420.21953510X-RAY DIFFRACTION98.52
2.93-3.090.28531450.22083592X-RAY DIFFRACTION98.71
3.09-3.280.28711430.21633547X-RAY DIFFRACTION98.66
3.28-3.530.25671450.19823585X-RAY DIFFRACTION98.86
3.53-3.890.2541450.18773590X-RAY DIFFRACTION98.78
3.89-4.450.22341440.16423542X-RAY DIFFRACTION98.42
4.45-5.60.22491430.1693561X-RAY DIFFRACTION97.99
5.6-29.990.17841450.15633581X-RAY DIFFRACTION99.44

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