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

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Basic information

Entry
Database: PDB / ID: 9mgx
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (phosphate/adenine 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
ADENINE / PHOSPHATE ION / Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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/adenine bound)
Authors: Mian, M.R. / 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)26,9094
Polymers26,6431
Non-polymers2663
Water4,810267
1
A: Purine nucleoside phosphorylase, putative
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)161,45424
Polymers159,8616
Non-polymers1,59318
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 area24550 Å2
ΔGint-249 kcal/mol
Surface area47430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.176, 93.176, 132.152
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-426-

HOH

21A-460-

HOH

31A-500-

HOH

41A-520-

HOH

51A-614-

HOH

61A-661-

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.: 1 / Source method: obtained synthetically / Formula: Cl
#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: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: JCSG+ C1: 20% (w/v) PEG 8000, 100 mM potassium phosphate citrate pH 4.2, 200 mM NaCl, TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. 4mM adenine added to the protein prior to crystallization. plate ...Details: JCSG+ C1: 20% (w/v) PEG 8000, 100 mM potassium phosphate citrate pH 4.2, 200 mM NaCl, TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. 4mM adenine added to the protein prior to crystallization. plate 14430 well C1 drop 3 , Puck: PSL1003. Cryo: 20% Glycerol + 80% crystallant

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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: 1.25→46.59 Å / Num. obs: 59488 / % possible obs: 97.5 % / Redundancy: 18 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.027 / Rrim(I) all: 0.12 / Χ2: 0.99 / Net I/σ(I): 13.8 / Num. measured all: 1067879
Reflection shellResolution: 1.25→1.27 Å / % possible obs: 79.5 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.829 / Num. measured all: 17955 / Num. unique obs: 2379 / CC1/2: 0.795 / Rpim(I) all: 0.308 / Rrim(I) all: 0.889 / Χ2: 1.01 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIXdev_5508refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→46.59 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1499 2956 4.98 %
Rwork0.1225 --
obs0.1239 59415 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 16 267 2102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071972
X-RAY DIFFRACTIONf_angle_d0.9942699
X-RAY DIFFRACTIONf_dihedral_angle_d11.423746
X-RAY DIFFRACTIONf_chiral_restr0.08309
X-RAY DIFFRACTIONf_plane_restr0.008351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.31431160.28252140X-RAY DIFFRACTION79
1.27-1.290.26361370.23532305X-RAY DIFFRACTION84
1.29-1.320.22191400.20592443X-RAY DIFFRACTION90
1.32-1.340.19971220.17722596X-RAY DIFFRACTION95
1.34-1.370.17361470.1412705X-RAY DIFFRACTION99
1.37-1.40.18141440.13462726X-RAY DIFFRACTION100
1.4-1.430.15251540.12422725X-RAY DIFFRACTION100
1.43-1.470.16461410.11832715X-RAY DIFFRACTION100
1.47-1.510.16791440.12232763X-RAY DIFFRACTION100
1.51-1.550.1521450.12922752X-RAY DIFFRACTION100
1.55-1.60.16731440.1252723X-RAY DIFFRACTION100
1.6-1.660.15291270.11322790X-RAY DIFFRACTION100
1.66-1.720.12651460.10052735X-RAY DIFFRACTION100
1.72-1.80.12091370.0982740X-RAY DIFFRACTION100
1.8-1.90.11971540.09652747X-RAY DIFFRACTION100
1.9-2.020.11881380.10332774X-RAY DIFFRACTION100
2.02-2.170.11981350.10312793X-RAY DIFFRACTION100
2.17-2.390.13131450.10782775X-RAY DIFFRACTION100
2.39-2.740.13771470.11192786X-RAY DIFFRACTION100
2.74-3.450.15331350.1172825X-RAY DIFFRACTION100
3.45-46.590.15971580.13832901X-RAY DIFFRACTION100

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