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- PDB-6b6k: Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 fr... -

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Basic information

Entry
Database: PDB / ID: 6b6k
TitleCrystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 6-methyl-2,3-dihydropyridazin-3-one
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE/INHIBITOR / Purine Nucleoside Phosphorylase / TRANSFERASE / TRANSFERASE-INHIBITOR complex
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
6-methylpyridazin-3-ol / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 3-methylpyridazin-1-ium-6-olate
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 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0939
Polymers31,4351
Non-polymers6578
Water3,765209
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)96,27827
Polymers94,3063
Non-polymers1,97124
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 area12750 Å2
ΔGint4 kcal/mol
Surface area30600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.700, 99.700, 99.700
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-541-

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.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-CVG / 6-methylpyridazin-3-ol


Mass: 110.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 53.18 %
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 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.46→70.5 Å / Num. obs: 57441 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.3
Reflection shellResolution: 1.46→1.5 Å / Redundancy: 10.7 % / Num. unique obs: 4464 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CXQ

5cxq


Resolution: 1.46→70.499 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 2824 4.92 %
Rwork0.1632 --
obs0.1642 57400 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→70.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 36 209 2395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012216
X-RAY DIFFRACTIONf_angle_d1.1122997
X-RAY DIFFRACTIONf_dihedral_angle_d13.986808
X-RAY DIFFRACTIONf_chiral_restr0.088347
X-RAY DIFFRACTIONf_plane_restr0.007386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4603-1.48550.34911530.30422728X-RAY DIFFRACTION100
1.4855-1.51250.29851370.2712711X-RAY DIFFRACTION100
1.5125-1.54160.26421210.24422670X-RAY DIFFRACTION100
1.5416-1.57310.23061630.21412704X-RAY DIFFRACTION100
1.5731-1.60730.22721160.21042744X-RAY DIFFRACTION100
1.6073-1.64470.20671450.1992666X-RAY DIFFRACTION100
1.6447-1.68580.20411350.19062728X-RAY DIFFRACTION100
1.6858-1.73140.2351490.17762699X-RAY DIFFRACTION100
1.7314-1.78240.18291690.17292708X-RAY DIFFRACTION100
1.7824-1.83990.19911220.15982693X-RAY DIFFRACTION100
1.8399-1.90570.18761820.1522702X-RAY DIFFRACTION100
1.9057-1.9820.19961310.16532702X-RAY DIFFRACTION100
1.982-2.07220.18581420.15262730X-RAY DIFFRACTION100
2.0722-2.18150.18951430.15372737X-RAY DIFFRACTION100
2.1815-2.31810.16571590.1492718X-RAY DIFFRACTION100
2.3181-2.49710.16791110.14492736X-RAY DIFFRACTION100
2.4971-2.74840.17251310.15212762X-RAY DIFFRACTION100
2.7484-3.14610.18621360.15882763X-RAY DIFFRACTION100
3.1461-3.96380.18671550.15552772X-RAY DIFFRACTION100
3.9638-70.58080.15611240.16312903X-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)
14.61293.84472.10438.10092.59874.69760.14250.096-1.01150.68050.0984-0.49510.8820.3044-0.16360.32030.03550.02380.1793-0.0350.367828.17812.556553.9442
22.4763-0.07510.94911.5653-0.37283.61220.13210.0595-0.6061-0.02830.03730.0780.6617-0.3687-0.13450.3766-0.08270.03790.2067-0.04590.406713.11149.263749.2978
35.8366-2.7403-5.40871.30752.62235.7361-0.03050.183-0.352-0.0605-0.15290.15670.0951-0.29170.1520.2327-0.02520.03180.145-0.00810.218917.094420.43455.2427
46.675-1.4172-0.57042.93151.34082.3605-0.03760.4387-0.0145-0.1868-0.18390.2519-0.0526-0.38340.19640.22-0.0401-0.02440.2312-0.00930.13292.211825.986244.083
51.39750.09830.17360.99990.29020.7729-0.03690.24450.0159-0.21910.00680.07820.0207-0.13840.0290.1977-0.03950.00110.1812-0.00660.12058.431530.684546.4293
68.217-2.5493-0.74392.93261.16030.87610.0051-0.2531-0.0858-0.0431-0.16320.43250.0377-0.22930.17090.1855-0.0514-0.00320.2478-0.0460.1648-2.906529.093749.4652
76.0295-1.8857-5.14192.47581.75744.4337-0.14620.0451-0.42960.014-0.01720.08150.3313-0.10490.14180.3171-0.0977-0.05360.3362-0.05820.25270.045115.84241.5811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 130 )
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 232 )
6X-RAY DIFFRACTION6chain 'A' and (resid 233 through 258 )
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 286 )

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