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- PDB-9mjq: Crystal structure of Purine nucleoside phosphorylase from Trichom... -

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Basic information

Entry
Database: PDB / ID: 9mjq
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (inosine bound)
ComponentsPurine nucleoside phosphorylase, putative
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Purine nucleoside phosphorylase / Trichomonas vaginalis
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
INOSINE / Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (inosine bound)
Authors: Ung, A.R. / Lovell, S. / Liu, L. / Battaile, K.P.
History
DepositionDec 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0185
Polymers26,6431
Non-polymers3754
Water3,549197
1
A: Purine nucleoside phosphorylase, putative
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)162,10830
Polymers159,8616
Non-polymers2,24824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area25900 Å2
ΔGint-321 kcal/mol
Surface area48100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.821, 92.821, 130.152
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-442-

HOH

31A-460-

HOH

41A-595-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase, putative


Mass: 26643.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_454490 / Plasmid: TrvaA.01033.d.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2EU62
#2: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: JCSG+ B5: 40% (v/v) MPD, 8% (w/v) PEG 8000, 100mM sodium cacodylate pH 6.5. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. cocrystallized with 2mM inosine. plate 14463 well B5 drop 1 , Puck: PSL0310, Cryo: direct.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 7, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.2→46.41 Å / Num. obs: 64325 / % possible obs: 95.6 % / Redundancy: 16.6 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.018 / Rrim(I) all: 0.079 / Χ2: 0.97 / Net I/σ(I): 19.7 / Num. measured all: 1068776
Reflection shellResolution: 1.2→1.22 Å / % possible obs: 67.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.864 / Num. measured all: 10803 / Num. unique obs: 2372 / CC1/2: 0.738 / Rpim(I) all: 0.445 / Rrim(I) all: 0.98 / Χ2: 0.96 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIXdev_5533refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→46.41 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1588 3165 4.92 %
Rwork0.1303 --
obs0.1317 64284 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 22 197 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061943
X-RAY DIFFRACTIONf_angle_d0.9222655
X-RAY DIFFRACTIONf_dihedral_angle_d13.71729
X-RAY DIFFRACTIONf_chiral_restr0.076310
X-RAY DIFFRACTIONf_plane_restr0.006340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.3599950.36741826X-RAY DIFFRACTION66
1.22-1.240.32941190.32872053X-RAY DIFFRACTION76
1.24-1.260.28171090.29922277X-RAY DIFFRACTION82
1.26-1.280.28611430.27062401X-RAY DIFFRACTION87
1.28-1.30.29961370.24982515X-RAY DIFFRACTION92
1.3-1.330.22341380.21732630X-RAY DIFFRACTION96
1.33-1.350.20241390.18442725X-RAY DIFFRACTION99
1.35-1.380.22141330.16322773X-RAY DIFFRACTION100
1.38-1.420.19681490.15062748X-RAY DIFFRACTION100
1.42-1.450.17761330.1362766X-RAY DIFFRACTION100
1.45-1.490.15581420.12542764X-RAY DIFFRACTION100
1.49-1.530.13721300.1232793X-RAY DIFFRACTION100
1.53-1.580.1541290.11712766X-RAY DIFFRACTION100
1.58-1.640.13341610.10632775X-RAY DIFFRACTION100
1.64-1.710.1471320.09752779X-RAY DIFFRACTION100
1.71-1.780.13271390.09192795X-RAY DIFFRACTION100
1.78-1.880.1091370.09362773X-RAY DIFFRACTION100
1.88-20.12211500.09362798X-RAY DIFFRACTION100
2-2.150.11431430.09432787X-RAY DIFFRACTION100
2.15-2.370.12141540.09862793X-RAY DIFFRACTION100
2.37-2.710.11941320.10622824X-RAY DIFFRACTION100
2.71-3.410.1541350.11872863X-RAY DIFFRACTION100
3.41-46.410.17061860.14042895X-RAY DIFFRACTION100

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