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

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Basic information

Entry
Database: PDB / ID: 9mfc
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (adenosine and phosphate 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
ADENOSINE / PHOSPHATE ION / Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 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 (adenosine and phosphate bound)
Authors: Lovell, S. / Liu, L. / Battaile, K.P.
History
DepositionDec 9, 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)27,0775
Polymers26,6431
Non-polymers4334
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.107, 93.107, 131.836
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-440-

HOH

21A-491-

HOH

31A-499-

HOH

41A-550-

HOH

51A-620-

HOH

61A-658-

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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: JCSG+ C1: 20% (w/v) PEG 8000, 100 mM potassium phosphate citriate pH 4.2, 20 mM NaCl. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. 2 mM adenosine added prior to crystallization. plate 14430 well ...Details: JCSG+ C1: 20% (w/v) PEG 8000, 100 mM potassium phosphate citriate pH 4.2, 20 mM NaCl. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. 2 mM adenosine added prior to crystallization. plate 14430 well C1 drop 1, Puck: PSL1001, Cryo: 80% crystallant + 20% PEG glycerol.

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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 20, 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: 1.24→46.55 Å / Num. obs: 61524 / % possible obs: 99 % / Redundancy: 17.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.022 / Rrim(I) all: 0.099 / Χ2: 0.99 / Net I/σ(I): 15.5 / Num. measured all: 1072439
Reflection shellResolution: 1.24→1.26 Å / % possible obs: 87.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.635 / Num. measured all: 16466 / Num. unique obs: 2649 / CC1/2: 0.894 / Rpim(I) all: 0.272 / Rrim(I) all: 0.694 / Χ2: 1.02 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIXdev_5493refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→46.55 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1477 3090 5.03 %
Rwork0.1293 --
obs0.1303 61463 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 26 261 2120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061998
X-RAY DIFFRACTIONf_angle_d0.982738
X-RAY DIFFRACTIONf_dihedral_angle_d13.894766
X-RAY DIFFRACTIONf_chiral_restr0.083316
X-RAY DIFFRACTIONf_plane_restr0.008353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.31551140.26052312X-RAY DIFFRACTION87
1.26-1.280.21111100.22452466X-RAY DIFFRACTION93
1.28-1.30.22931450.18692584X-RAY DIFFRACTION97
1.3-1.330.20281240.16982632X-RAY DIFFRACTION98
1.33-1.350.18191380.15852651X-RAY DIFFRACTION99
1.35-1.380.16781510.14482642X-RAY DIFFRACTION100
1.38-1.410.19811400.13472665X-RAY DIFFRACTION100
1.41-1.440.16231340.12492675X-RAY DIFFRACTION100
1.44-1.480.16611520.12662675X-RAY DIFFRACTION100
1.48-1.520.16621310.12582652X-RAY DIFFRACTION100
1.52-1.560.14121400.1332672X-RAY DIFFRACTION100
1.56-1.610.16341570.12952681X-RAY DIFFRACTION100
1.61-1.670.15991390.12612649X-RAY DIFFRACTION100
1.67-1.740.14881230.11512719X-RAY DIFFRACTION100
1.74-1.820.14451410.11812674X-RAY DIFFRACTION100
1.82-1.910.12571600.11152669X-RAY DIFFRACTION100
1.91-2.030.13481410.11542684X-RAY DIFFRACTION100
2.03-2.190.11481250.10972718X-RAY DIFFRACTION100
2.19-2.410.11831400.11252704X-RAY DIFFRACTION100
2.41-2.760.12641600.12292705X-RAY DIFFRACTION100
2.76-3.470.13511630.12512719X-RAY DIFFRACTION100
3.47-46.550.16041620.1372825X-RAY DIFFRACTION100

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