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- PDB-6b3l: Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 fr... -

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Basic information

Entry
Database: PDB / ID: 6b3l
TitleCrystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 2,3-dihydro-1H-inden-2-amine
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 / 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
INDAN-2-AMINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.52 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 2,3-dihydro-1H-inden-2-amine
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 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,0378
Polymers31,4351
Non-polymers6027
Water4,360242
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)96,11224
Polymers94,3063
Non-polymers1,80621
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 area11900 Å2
ΔGint-15 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.910, 99.910, 99.910
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-578-

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.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-XM0 / INDAN-2-AMINE


Mass: 133.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / 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 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.52→49.96 Å / Num. obs: 51238 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 1 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.7
Reflection shellResolution: 1.52→1.56 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3731 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
Cootmodel building
PHENIXphasing
XDSdata scaling
RefinementResolution: 1.52→49.955 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 2518 4.92 %
Rwork0.1659 --
obs0.1674 51202 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→49.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 34 242 2426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012239
X-RAY DIFFRACTIONf_angle_d1.0593030
X-RAY DIFFRACTIONf_dihedral_angle_d11.1971346
X-RAY DIFFRACTIONf_chiral_restr0.068350
X-RAY DIFFRACTIONf_plane_restr0.007390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5204-1.54970.30811410.28842664X-RAY DIFFRACTION100
1.5497-1.58130.29511430.26522654X-RAY DIFFRACTION100
1.5813-1.61570.27571210.24122712X-RAY DIFFRACTION100
1.6157-1.65330.22791380.22682682X-RAY DIFFRACTION100
1.6533-1.69460.23161410.20812671X-RAY DIFFRACTION100
1.6946-1.74050.24171470.20222669X-RAY DIFFRACTION100
1.7405-1.79170.20891620.18272674X-RAY DIFFRACTION100
1.7917-1.84950.18591330.17972687X-RAY DIFFRACTION100
1.8495-1.91560.17761740.16862670X-RAY DIFFRACTION100
1.9156-1.99230.19621250.15712703X-RAY DIFFRACTION100
1.9923-2.0830.1951440.14962697X-RAY DIFFRACTION100
2.083-2.19280.17651390.1492678X-RAY DIFFRACTION100
2.1928-2.33020.18521590.14772688X-RAY DIFFRACTION100
2.3302-2.51010.18611060.15232767X-RAY DIFFRACTION100
2.5101-2.76270.20561340.15522708X-RAY DIFFRACTION100
2.7627-3.16240.2061380.14962730X-RAY DIFFRACTION100
3.1624-3.9840.17731490.15492765X-RAY DIFFRACTION100
3.984-49.9820.1981240.16462865X-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)
15.70454.16341.01819.65412.9253.7771-0.15060.1872-0.74390.22530.2789-0.6330.49920.3467-0.16820.1770.01950.0450.120.00520.178829.169311.878553.1843
24.3016-0.66442.33741.8758-1.87433.26220.0248-0.1266-0.45360.01770.05330.22990.4087-0.3484-0.03840.2143-0.04020.04550.1435-0.03020.250214.30149.151349.2405
35.3537-3.6003-5.09662.32613.50796.8643-0.14580.0342-0.41650.0344-0.02620.28960.0583-0.15830.1440.1399-0.01410.0210.08620.0140.159317.715620.444355.5394
49.4232-4.314-1.89314.0231.79071.68910.12730.6182-0.0762-0.2981-0.26130.2711-0.1823-0.30610.16640.1649-0.0046-0.03370.1797-0.00240.09582.332925.978844.3064
51.5188-0.05080.31790.85710.32710.7032-0.00280.2511-0.0483-0.21820.01080.0573-0.0213-0.03880.04250.1482-0.0191-0.00540.13720.00360.092911.29129.471143.2636
62.5709-1.1826-0.94750.63390.71690.90660.05380.07070.0823-0.1155-0.0474-0.0046-0.0838-0.1049-0.01010.1687-0.0185-0.00470.1629-0.00930.13934.732533.037953.387
79.7004-3.8028-2.24042.01541.47481.0194-0.0603-0.3492-0.3492-0.0028-0.09170.30360.0601-0.1370.17380.1464-0.038-0.00570.2146-0.02220.1492-2.340928.808849.8363
88.5328-2.9973-6.394.65823.11883.18-0.2442-0.2303-0.53490.2210.07060.25010.35620.27130.2760.208-0.0522-0.0790.2452-0.01120.20240.150715.566541.8567
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 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 196 )
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 232 )
7X-RAY DIFFRACTION7chain 'A' and (resid 233 through 258 )
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 285 )

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