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

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Basic information

Entry
Database: PDB / ID: 6bhb
TitleCrystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 2-aminopyrimidin-5-ol
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / Purine Nucleoside Phosphorylase
Function / homology
Function and homology information


guanosine phosphorylase activity / nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / 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
2-aminopyrimidin-5-ol / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 2-aminopyrimidin-5-ol
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
DepositionOct 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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)32,17210
Polymers31,4351
Non-polymers7369
Water1,54986
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)96,51530
Polymers94,3063
Non-polymers2,20827
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 area12900 Å2
ΔGint2 kcal/mol
Surface area30060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.740, 99.740, 99.740
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-473-

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): Lemo21 (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-DS1 / 2-aminopyrimidin-5-ol


Mass: 111.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M Ammonium Acetate , 0.1 M Bis-Tris, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2→70.53 Å / Num. obs: 22643 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 1 / Rmerge(I) obs: 0.132 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1671 / CC1/2: 0.6 / % possible all: 100

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Processing

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

5cxq


Resolution: 2→70.53 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.78
RfactorNum. reflection% reflection
Rfree0.2135 1078 4.77 %
Rwork0.1847 --
obs0.186 22615 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→70.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 40 86 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022211
X-RAY DIFFRACTIONf_angle_d0.5842991
X-RAY DIFFRACTIONf_dihedral_angle_d10.7181314
X-RAY DIFFRACTIONf_chiral_restr0.047347
X-RAY DIFFRACTIONf_plane_restr0.004385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0008-2.09190.27931590.25382643X-RAY DIFFRACTION100
2.0919-2.20220.23831350.22492654X-RAY DIFFRACTION100
2.2022-2.34010.24871420.20382653X-RAY DIFFRACTION100
2.3401-2.52080.22131040.19542703X-RAY DIFFRACTION100
2.5208-2.77450.23361370.19142672X-RAY DIFFRACTION100
2.7745-3.1760.21031380.19362666X-RAY DIFFRACTION100
3.176-4.00120.23271390.17882719X-RAY DIFFRACTION100
4.0012-57.60880.17081240.16162827X-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)
17.66113.1645-0.92155.94683.16087.8485-0.04920.1508-1.16290.330.3364-0.87361.04850.6419-0.34940.34260.0575-0.00270.2475-0.02450.399127.958311.691152.7722
24.1047-1.18850.71725.0814-1.05584.21770.51470.1119-0.89420.0938-0.18170.1450.4708-0.3156-0.31120.521-0.0987-0.0140.291-0.04930.496411.41348.815946.8647
33.84671.6935-5.69243.253-2.30288.6445-0.3971-0.3845-0.16240.50370.45170.62730.4421-0.6947-0.05950.5397-0.05270.03420.37980.05170.429915.362712.200461.2489
45.12391.07440.98819.1417-5.68424.1215-0.01430.1695-0.86870.08480.00010.05571.4701-0.4718-0.00550.413-0.07220.03750.3489-0.09890.449313.67778.813643.5632
56.6038-2.69-6.08751.09482.61776.50870.046-0.1182-0.06280.04880.00690.11560.15220.0611-0.03530.3425-0.05260.03240.2333-0.02070.291916.799420.712755.6646
62.5416-0.2956-0.121.24680.29260.70590.04930.35690.0172-0.2242-0.01960.01490.0291-0.031-0.02870.2926-0.03560.02530.3089-0.00140.217512.577929.812347.195
71.7742-0.5341-0.0384.13283.85777.7781-0.1450.5178-0.045-0.6858-0.20940.4847-0.1342-0.40440.19650.3667-0.0684-0.05160.4425-0.00270.2351.449825.770834.9713
82.4856-0.7863-1.13042.50131.46732.3366-0.01550.01740.0872-0.1034-0.04580.1567-0.0159-0.25580.12190.2242-0.0502-0.01190.2416-0.02240.17244.755132.966752.9289
97.3764-1.5733-0.69122.25670.89920.34770.07120.1193-0.1603-0.0645-0.15630.25730.0475-0.25870.13080.2788-0.0356-0.01950.3303-0.03230.2541-3.841629.127649.6247
106.1841-1.7627-4.23544.45793.70618.433-0.15590.415-0.66160.0488-0.13870.05210.4358-0.52270.26930.3539-0.1015-0.07080.3746-0.04260.3282-0.6116.009441.9997
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 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 84 )
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 107 )
6X-RAY DIFFRACTION6chain 'A' and (resid 108 through 169 )
7X-RAY DIFFRACTION7chain 'A' and (resid 170 through 196 )
8X-RAY DIFFRACTION8chain 'A' and (resid 197 through 233 )
9X-RAY DIFFRACTION9chain 'A' and (resid 234 through 258 )
10X-RAY DIFFRACTION10chain 'A' and (resid 259 through 285 )

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