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

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Basic information

Entry
Database: PDB / ID: 9mis
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (P21 form)
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
CITRATE ANION / Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 (P21 form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 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
B: Purine nucleoside phosphorylase, putative
C: Purine nucleoside phosphorylase, putative
D: Purine nucleoside phosphorylase, putative
E: Purine nucleoside phosphorylase, putative
F: Purine nucleoside phosphorylase, putative
G: Purine nucleoside phosphorylase, putative
H: Purine nucleoside phosphorylase, putative
I: Purine nucleoside phosphorylase, putative
J: Purine nucleoside phosphorylase, putative
K: Purine nucleoside phosphorylase, putative
L: Purine nucleoside phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,47816
Polymers319,72112
Non-polymers7564
Water61,0533389
1
A: Purine nucleoside phosphorylase, putative
B: Purine nucleoside phosphorylase, putative
C: Purine nucleoside phosphorylase, putative
D: Purine nucleoside phosphorylase, putative
E: Purine nucleoside phosphorylase, putative
F: Purine nucleoside phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,2398
Polymers159,8616
Non-polymers3782
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19910 Å2
ΔGint-154 kcal/mol
Surface area47360 Å2
MethodPISA
2
G: Purine nucleoside phosphorylase, putative
H: Purine nucleoside phosphorylase, putative
I: Purine nucleoside phosphorylase, putative
J: Purine nucleoside phosphorylase, putative
K: Purine nucleoside phosphorylase, putative
L: Purine nucleoside phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,2398
Polymers159,8616
Non-polymers3782
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint-152 kcal/mol
Surface area47100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.491, 50.821, 193.139
Angle α, β, γ (deg.)90.00, 111.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Purine nucleoside phosphorylase, putative


Mass: 26643.428 Da / Num. of mol.: 12
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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3389 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ A2: 0.2 M citrate pH 5.5, 20% (w/v) PEG 3000. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. citrate acquired from the crystallant in 4 of the subunits. plate 14463 well A2 drop 2 , Puck: ...Details: JCSG+ A2: 0.2 M citrate pH 5.5, 20% (w/v) PEG 3000. TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. citrate acquired from the crystallant in 4 of the subunits. plate 14463 well A2 drop 2 , Puck: PSL1212, 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 26, 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: 1.59→48.89 Å / Num. obs: 428168 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.051 / Rrim(I) all: 0.135 / Χ2: 1 / Net I/σ(I): 10.9 / Num. measured all: 2933246
Reflection shellResolution: 1.59→1.63 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.21 / Num. measured all: 222566 / Num. unique obs: 31456 / CC1/2: 0.581 / Rpim(I) all: 0.487 / Rrim(I) all: 1.306 / Χ2: 0.82 / 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: 1.59→48.01 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 21497 5.02 %
Rwork0.1509 --
obs0.1522 427998 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21516 0 52 3389 24957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522693
X-RAY DIFFRACTIONf_angle_d0.78330977
X-RAY DIFFRACTIONf_dihedral_angle_d13.0838443
X-RAY DIFFRACTIONf_chiral_restr0.0513600
X-RAY DIFFRACTIONf_plane_restr0.0074033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.27857170.258613333X-RAY DIFFRACTION100
1.61-1.630.28257130.252613516X-RAY DIFFRACTION100
1.63-1.650.27927110.245113433X-RAY DIFFRACTION100
1.65-1.670.26697080.2413435X-RAY DIFFRACTION100
1.67-1.690.25957190.228913554X-RAY DIFFRACTION100
1.69-1.710.24267170.214413362X-RAY DIFFRACTION100
1.71-1.740.24157160.212713544X-RAY DIFFRACTION100
1.74-1.760.23467470.204613477X-RAY DIFFRACTION100
1.76-1.790.22286920.192113400X-RAY DIFFRACTION100
1.79-1.820.21017260.187913631X-RAY DIFFRACTION100
1.82-1.850.2067450.17813372X-RAY DIFFRACTION100
1.85-1.890.19327000.170313586X-RAY DIFFRACTION100
1.89-1.920.21337260.172413411X-RAY DIFFRACTION100
1.92-1.960.1986720.165913626X-RAY DIFFRACTION100
1.96-20.19636860.169313405X-RAY DIFFRACTION100
2-2.050.17947510.150513519X-RAY DIFFRACTION100
2.05-2.10.16887190.143113583X-RAY DIFFRACTION100
2.1-2.160.16737310.143413439X-RAY DIFFRACTION100
2.16-2.220.16527000.139913620X-RAY DIFFRACTION100
2.22-2.290.17257010.137713531X-RAY DIFFRACTION100
2.29-2.380.16797100.13513534X-RAY DIFFRACTION100
2.38-2.470.17687560.135713498X-RAY DIFFRACTION100
2.47-2.580.17017030.135913596X-RAY DIFFRACTION100
2.58-2.720.15917240.1313598X-RAY DIFFRACTION100
2.72-2.890.15357220.132913614X-RAY DIFFRACTION100
2.89-3.110.17437080.139513644X-RAY DIFFRACTION100
3.11-3.430.15346760.13313705X-RAY DIFFRACTION100
3.43-3.920.15087180.129613729X-RAY DIFFRACTION100
3.92-4.940.11867090.110413748X-RAY DIFFRACTION100
4.94-48.010.1887740.164814058X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 114.6306 Å / Origin y: -10.5721 Å / Origin z: 45.3148 Å
111213212223313233
T0.144 Å2-0.0146 Å20.0096 Å2-0.0901 Å2-0.0032 Å2--0.1059 Å2
L0.4241 °2-0.1 °20.1684 °2-0.0677 °2-0.0378 °2--0.0668 °2
S0.0014 Å °0.0264 Å °-0.0005 Å °-0.002 Å °-0.0091 Å °-0.002 Å °0.0034 Å °0.0098 Å °0.0066 Å °
Refinement TLS groupSelection details: all

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