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- PDB-6axa: Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 fr... -

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Basic information

Entry
Database: PDB / ID: 6axa
TitleCrystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with (3S)-5-fluoro-3-hydroxy-1,3-dihydroindol-2-one
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / Purine Nucleoside Phosphorylase
Function / homology
Function and homology information


nucleoside metabolic process / guanosine phosphorylase activity / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / cytoplasm
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-D4Y / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsFaheem, M. / Neto, J.B. / Collins, P. / Pearce, N.M. / Valadares, N.F. / Bird, L. / Pereira, H.M. / Delft, F.V. / Barbosa, J.A.R.G.
CitationJournal: To Be Published
Title: Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 5-fluoro-3-hydroxy-1,3-dihydroindol-2-one
Authors: Faheem, M. / Neto, J.B. / Collins, P. / Pearce, N.M. / Valadares, N.F. / Bird, L. / Pereira, H.M. / Delft, F.V. / Barbosa, J.A.R.G.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,22810
Polymers31,4351
Non-polymers7929
Water3,999222
1
A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,68330
Polymers94,3063
Non-polymers2,37727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area13060 Å2
ΔGint-5 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.930, 99.930, 99.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21A-590-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase / Inosine-guanosine phosphorylase


Mass: 31435.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0U3AGT1, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-D4Y / (3S)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one


Mass: 167.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6FNO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium Acetate, Bis-Tris , PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.59→70.661 Å / Num. obs: 44906 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 1 / Net I/σ(I): 12.3
Reflection shellResolution: 1.59→1.63 Å / Num. unique obs: 3299

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CXQ

5cxq


Resolution: 1.59→70.661 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 2189 4.88 %
Rwork0.1632 --
obs0.164 44875 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→70.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 44 222 2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132215
X-RAY DIFFRACTIONf_angle_d1.1853001
X-RAY DIFFRACTIONf_dihedral_angle_d11.8051342
X-RAY DIFFRACTIONf_chiral_restr0.076349
X-RAY DIFFRACTIONf_plane_restr0.008386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5902-1.62480.30531230.282646X-RAY DIFFRACTION100
1.6248-1.66260.28961080.2592688X-RAY DIFFRACTION100
1.6626-1.70420.25691610.23762590X-RAY DIFFRACTION100
1.7042-1.75020.26121430.22472643X-RAY DIFFRACTION100
1.7502-1.80170.21871470.20972637X-RAY DIFFRACTION100
1.8017-1.85990.22221510.18952643X-RAY DIFFRACTION100
1.8599-1.92640.19351530.17582642X-RAY DIFFRACTION100
1.9264-2.00350.21081230.16832633X-RAY DIFFRACTION100
2.0035-2.09470.19921590.15382633X-RAY DIFFRACTION100
2.0947-2.20520.18041370.15182672X-RAY DIFFRACTION100
2.2052-2.34330.16051420.14282635X-RAY DIFFRACTION100
2.3433-2.52430.19121040.14962716X-RAY DIFFRACTION100
2.5243-2.77830.19291370.15272684X-RAY DIFFRACTION100
2.7783-3.18030.1621360.14972672X-RAY DIFFRACTION100
3.1803-4.00680.16361410.14892724X-RAY DIFFRACTION100
4.0068-70.7310.15871240.16482828X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.69462.9281.20893.12752.79685.35050.08820.1819-1.0010.17990.1562-0.70920.80420.4973-0.1910.32190.06690.02220.204-0.03850.392328.080712.23753.1135
23.7663-0.3542.31892.4967-0.22192.71530.2586-0.1267-0.81420.0797-0.02090.21060.673-0.3782-0.15960.4317-0.06370.02370.233-0.02540.476213.10099.60151.1577
32.7558-0.97020.23836.4819-1.53181.9980.01680.3998-0.6283-0.27350.0566-0.02170.8326-0.1508-0.02360.3818-0.05610.0260.3233-0.14090.48113.81488.978843.7357
49.0076-3.0981-6.19361.07582.1565.63750.03080.1508-0.447-0.0872-0.13380.11460.0651-0.18750.11220.247-0.00770.020.1459-0.00390.234317.012420.68255.4196
57.6646-2.3234-0.75453.43061.11322.11940.07560.598-0.1943-0.2529-0.24140.2953-0.0338-0.320.08950.2443-0.0322-0.03320.2669-0.00970.15392.240326.168144.1307
61.76630.01750.19371.26670.36050.9098-0.00670.2692-0.0294-0.2426-0.04370.12030.0317-0.1460.06130.2182-0.0277-0.00570.2197-0.01450.15596.28530.464947.1318
74.3175-1.97-5.54332.49832.08537.3376-0.0855-0.0484-0.42120.0069-0.04090.14490.43840.10660.32110.3501-0.0925-0.07830.3931-0.11170.3126-0.391915.959442.0381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 108 )
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 130 )
6X-RAY DIFFRACTION6chain 'A' and (resid 131 through 258 )
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 285 )

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