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

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Basic information

Entry
Database: PDB / ID: 9mgj
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (mannose 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
alpha-D-mannopyranose / Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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 (mannose bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9163
Polymers26,6431
Non-polymers2722
Water4,720262
1
A: Purine nucleoside phosphorylase, putative
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,49418
Polymers159,8616
Non-polymers1,63412
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 area24290 Å2
ΔGint-126 kcal/mol
Surface area48490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.012, 93.012, 130.529
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-419-

HOH

21A-427-

HOH

31A-506-

HOH

41A-615-

HOH

51A-659-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: Morpheus F4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose and ...Details: Morpheus F4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM D-Glucose, 20 mM D-Mannose, 20 mM D-Galactose, 20 mM L-Fucose, 20 mM D-Xylose and 20 mM N-Acetyl-D-Glucosamine. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. mannose acquired from the crystallant. plate 14431 well H8 drop 3, Puck: PSL0916. 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: Oct 24, 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: 1.18→68.55 Å / Num. obs: 66110 / % possible obs: 92.8 % / Redundancy: 16.5 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.014 / Rrim(I) all: 0.062 / Χ2: 0.93 / Net I/σ(I): 21.9 / Num. measured all: 1087763
Reflection shellResolution: 1.18→1.21 Å / % possible obs: 52.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.512 / Num. measured all: 11671 / Num. unique obs: 2743 / CC1/2: 0.892 / Rpim(I) all: 0.272 / Rrim(I) all: 0.585 / Χ2: 0.77 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIXdev_5438refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→46.51 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1467 3268 4.95 %
Rwork0.1275 --
obs0.1284 65994 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.18→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 18 262 2113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062013
X-RAY DIFFRACTIONf_angle_d0.9522757
X-RAY DIFFRACTIONf_dihedral_angle_d11.454790
X-RAY DIFFRACTIONf_chiral_restr0.079322
X-RAY DIFFRACTIONf_plane_restr0.007353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.20.3699660.33611387X-RAY DIFFRACTION47
1.2-1.220.29471020.30961771X-RAY DIFFRACTION61
1.22-1.240.27541110.27522114X-RAY DIFFRACTION73
1.24-1.260.26981260.24722320X-RAY DIFFRACTION80
1.26-1.280.2441230.2232507X-RAY DIFFRACTION85
1.28-1.310.23551310.20012653X-RAY DIFFRACTION91
1.31-1.330.19951420.17762801X-RAY DIFFRACTION95
1.33-1.360.22861540.15042880X-RAY DIFFRACTION99
1.36-1.390.16241370.13842916X-RAY DIFFRACTION100
1.39-1.430.1621450.13242932X-RAY DIFFRACTION100
1.43-1.470.15921700.12282921X-RAY DIFFRACTION100
1.47-1.510.16621340.12362922X-RAY DIFFRACTION100
1.51-1.560.15541760.11922911X-RAY DIFFRACTION100
1.56-1.610.14491570.11472925X-RAY DIFFRACTION100
1.61-1.680.13361440.11542938X-RAY DIFFRACTION100
1.68-1.750.13211730.11032935X-RAY DIFFRACTION100
1.75-1.850.14981540.11112919X-RAY DIFFRACTION100
1.85-1.960.11261530.11112963X-RAY DIFFRACTION100
1.96-2.110.12981500.1092970X-RAY DIFFRACTION100
2.11-2.330.131500.10892966X-RAY DIFFRACTION100
2.33-2.660.13461530.11252977X-RAY DIFFRACTION100
2.66-3.360.12541600.11632991X-RAY DIFFRACTION100
3.36-46.510.13771570.1253107X-RAY DIFFRACTION100

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