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

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Basic information

Entry
Database: PDB / ID: 9mgo
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (citrate 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
CITRIC ACID / Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 (citrate bound)
Authors: 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,01312
Polymers159,8616
Non-polymers1,1536
Water16,159897
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22000 Å2
ΔGint-148 kcal/mol
Surface area47530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.708, 148.782, 92.987
Angle α, β, γ (deg.)90.00, 92.69, 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.: 6
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 897 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: Index D4: 0.1M Citric acid pH 3.5, 25% PEG 3350, TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. citrate acquired from the crystallant. plate 14433 well D4 drop 2 , Puck: PSL0912. 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: 1.89→148.78 Å / Num. obs: 111774 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.053 / Rrim(I) all: 0.13 / Χ2: 1.1 / Net I/σ(I): 11.1 / Num. measured all: 646415
Reflection shellResolution: 1.89→1.94 Å / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 1.275 / Num. measured all: 47584 / Num. unique obs: 8279 / CC1/2: 0.711 / Rpim(I) all: 0.574 / Rrim(I) all: 1.402 / Χ2: 0.94 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIXdev_5508refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→74.39 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 5578 4.99 %
Rwork0.1613 --
obs0.163 111687 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→74.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10764 0 78 897 11739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111082
X-RAY DIFFRACTIONf_angle_d1.06515056
X-RAY DIFFRACTIONf_dihedral_angle_d11.8384026
X-RAY DIFFRACTIONf_chiral_restr0.0611744
X-RAY DIFFRACTIONf_plane_restr0.0091950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.910.3131990.27713552X-RAY DIFFRACTION100
1.91-1.930.28552150.26553510X-RAY DIFFRACTION100
1.93-1.960.27451850.24243475X-RAY DIFFRACTION100
1.96-1.980.27161850.23943569X-RAY DIFFRACTION100
1.98-2.010.28931730.23173551X-RAY DIFFRACTION100
2.01-2.040.27351920.22113501X-RAY DIFFRACTION100
2.04-2.070.24231790.21393577X-RAY DIFFRACTION100
2.07-2.10.25981740.1963485X-RAY DIFFRACTION100
2.1-2.130.2781750.19363556X-RAY DIFFRACTION100
2.13-2.160.22881840.18753572X-RAY DIFFRACTION100
2.16-2.20.23321680.18153444X-RAY DIFFRACTION100
2.2-2.240.24212150.17543561X-RAY DIFFRACTION100
2.24-2.280.2272060.17123479X-RAY DIFFRACTION100
2.28-2.330.22531620.17033604X-RAY DIFFRACTION100
2.33-2.380.20561790.16323534X-RAY DIFFRACTION100
2.38-2.440.19571760.16123553X-RAY DIFFRACTION100
2.44-2.50.20791900.15663500X-RAY DIFFRACTION100
2.5-2.570.20321940.15913556X-RAY DIFFRACTION100
2.57-2.640.1941850.15253514X-RAY DIFFRACTION100
2.64-2.730.2241930.15543551X-RAY DIFFRACTION100
2.73-2.820.2131780.15513526X-RAY DIFFRACTION100
2.82-2.940.19231780.15523526X-RAY DIFFRACTION100
2.94-3.070.21122010.16163560X-RAY DIFFRACTION100
3.07-3.230.20351900.15843544X-RAY DIFFRACTION100
3.23-3.430.15791900.15083518X-RAY DIFFRACTION100
3.43-3.70.1641740.14533557X-RAY DIFFRACTION100
3.7-4.070.1611800.13493511X-RAY DIFFRACTION99
4.07-4.660.12832170.11573544X-RAY DIFFRACTION100
4.66-5.870.15621950.13993544X-RAY DIFFRACTION100
5.87-74.390.19591460.17263635X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 9.7928 Å / Origin y: 8.476 Å / Origin z: -19.3475 Å
111213212223313233
T0.2041 Å2-0.0251 Å2-0.0131 Å2-0.153 Å2-0.0071 Å2--0.1689 Å2
L0.2672 °2-0.1253 °2-0.1354 °2-0.4694 °20.1555 °2--0.6112 °2
S-0.0196 Å °0.0437 Å °-0.0274 Å °0.0227 Å °-0.015 Å °0.0222 Å °-0.0512 Å °-0.0085 Å °0.0326 Å °
Refinement TLS groupSelection details: all

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