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- PDB-9mg7: Crystal structure of Purine nucleoside phosphorylase from Trichom... -

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Basic information

Entry
Database: PDB / ID: 9mg7
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (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
PHOSPHATE ION / Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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 (phosphate bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 10, 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

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8303
Polymers26,6431
Non-polymers1872
Water4,450247
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)93.391, 93.391, 132.570
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-436-

HOH

21A-490-

HOH

31A-492-

HOH

41A-604-

HOH

51A-606-

HOH

61A-646-

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: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: JCSG+ B6: 0.1 M potassium phosphate/citrate, pH 4.2, 40% (v/v) etahnol, 5% (w/v) PEG 1000. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. phosphate acquired from the crystallization. plate 14462 ...Details: JCSG+ B6: 0.1 M potassium phosphate/citrate, pH 4.2, 40% (v/v) etahnol, 5% (w/v) PEG 1000. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. phosphate acquired from the crystallization. plate 14462 well C8 drop 1, Puck: PSL1213, Cryo: 80% crystallant + 20% 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 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: 1.27→46.7 Å / Num. obs: 57938 / % possible obs: 98.8 % / Redundancy: 18 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.018 / Rrim(I) all: 0.08 / Χ2: 1.01 / Net I/σ(I): 23.8 / Num. measured all: 1043673
Reflection shellResolution: 1.27→1.3 Å / % possible obs: 88.5 % / Redundancy: 8 % / Rmerge(I) obs: 1.007 / Num. measured all: 30497 / Num. unique obs: 3793 / CC1/2: 0.713 / Rpim(I) all: 0.366 / Rrim(I) all: 1.076 / Χ2: 0.8 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIXdev_5438refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→46.7 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1614 2902 5.01 %
Rwork0.1394 --
obs0.1405 57918 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 11 247 2081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061943
X-RAY DIFFRACTIONf_angle_d0.9232652
X-RAY DIFFRACTIONf_dihedral_angle_d12.526727
X-RAY DIFFRACTIONf_chiral_restr0.078305
X-RAY DIFFRACTIONf_plane_restr0.009343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.290.34341450.31032249X-RAY DIFFRACTION86
1.29-1.310.33791380.30392422X-RAY DIFFRACTION92
1.31-1.340.2811390.25732514X-RAY DIFFRACTION96
1.34-1.360.24211290.22462623X-RAY DIFFRACTION99
1.36-1.390.23791160.19882636X-RAY DIFFRACTION100
1.39-1.420.19631400.17992662X-RAY DIFFRACTION100
1.42-1.450.19641380.15662625X-RAY DIFFRACTION100
1.45-1.490.18351460.15292605X-RAY DIFFRACTION100
1.49-1.530.19331410.14032627X-RAY DIFFRACTION100
1.53-1.580.1541330.12742645X-RAY DIFFRACTION100
1.58-1.630.15771390.12592644X-RAY DIFFRACTION100
1.63-1.680.15811480.12092628X-RAY DIFFRACTION100
1.68-1.750.16381270.12032661X-RAY DIFFRACTION100
1.75-1.830.15441380.11992655X-RAY DIFFRACTION100
1.83-1.930.15731420.12812650X-RAY DIFFRACTION100
1.93-2.050.15491490.12422650X-RAY DIFFRACTION100
2.05-2.210.13341450.11812649X-RAY DIFFRACTION100
2.21-2.430.14161300.12252675X-RAY DIFFRACTION100
2.43-2.780.15941340.12322697X-RAY DIFFRACTION100
2.78-3.50.12751310.13232713X-RAY DIFFRACTION100
3.5-46.70.14611540.13372786X-RAY DIFFRACTION100

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