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- PDB-9mh2: Crystal structure of Purine nucleoside phosphorylase from Trichom... -

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Basic information

Entry
Database: PDB / ID: 9mh2
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (Adenosine and glycine complex)
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 / GLYCINE / Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 glycine complex)
Authors: Seibold, S. / 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)27,0965
Polymers26,6431
Non-polymers4534
Water3,549197
1
A: Purine nucleoside phosphorylase, putative
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)162,57830
Polymers159,8616
Non-polymers2,71724
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 area24250 Å2
ΔGint-211 kcal/mol
Surface area46950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.033, 93.033, 130.449
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-430-

HOH

21A-474-

HOH

31A-582-

HOH

41A-596-

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-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#5: 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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus H8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride ...Details: Morpheus H8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine. TrvaA.00429.d.B1.PW39248 at 25 mg/mL. 2mM adenosine added to protein prior to crystallization. plate 14431 well H8 drop 1 . Puck: PSL-0914, 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 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: 1.35→46.52 Å / Num. obs: 47748 / % possible obs: 100 % / Redundancy: 16.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.022 / Rrim(I) all: 0.091 / Χ2: 1.01 / Net I/σ(I): 15.2 / Num. measured all: 785386
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 99.8 % / Redundancy: 11.3 % / Rmerge(I) obs: 1.56 / Num. measured all: 26050 / Num. unique obs: 2307 / CC1/2: 0.882 / Rpim(I) all: 0.482 / Rrim(I) all: 1.634 / Χ2: 1.03 / 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: 1.35→46.52 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1681 2372 4.98 %
Rwork0.1418 --
obs0.1431 47635 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 30 197 2046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061938
X-RAY DIFFRACTIONf_angle_d0.8662644
X-RAY DIFFRACTIONf_dihedral_angle_d14.402734
X-RAY DIFFRACTIONf_chiral_restr0.073306
X-RAY DIFFRACTIONf_plane_restr0.007340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.38011600.35582615X-RAY DIFFRACTION100
1.38-1.410.33161280.31142634X-RAY DIFFRACTION100
1.41-1.440.27441290.23252656X-RAY DIFFRACTION100
1.44-1.480.24451470.1922610X-RAY DIFFRACTION100
1.48-1.520.21191280.17722643X-RAY DIFFRACTION99
1.52-1.560.2271210.17712625X-RAY DIFFRACTION99
1.56-1.610.22651440.16362664X-RAY DIFFRACTION100
1.61-1.670.23081310.13322643X-RAY DIFFRACTION100
1.67-1.740.15111320.13162644X-RAY DIFFRACTION100
1.74-1.810.16061370.12842665X-RAY DIFFRACTION100
1.81-1.910.16871600.12082643X-RAY DIFFRACTION100
1.91-2.030.1581520.12882659X-RAY DIFFRACTION100
2.03-2.190.14951220.12152667X-RAY DIFFRACTION100
2.19-2.410.15751300.12912697X-RAY DIFFRACTION100
2.41-2.750.15941470.13252696X-RAY DIFFRACTION100
2.76-3.470.17111390.13712711X-RAY DIFFRACTION100
3.47-46.520.13561650.12872791X-RAY DIFFRACTION100

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