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- PDB-3djf: Crystal Structure of Schistosoma mansoni Purine Nucleoside Phosph... -

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Basic information

Entry
Database: PDB / ID: 3djf
TitleCrystal Structure of Schistosoma mansoni Purine Nucleoside Phosphorylase in a complex with BCX-34
ComponentsPurine-nucleoside phosphorylase
KeywordsTRANSFERASE / Purine Nucleoside Phosphorylase / BCX34 / Inhibitor / Glycosyltransferase
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
Chem-BC3 / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.302 Å
AuthorsPostigo, M.P. / Pereira, H.M. / Oliva, G. / Andricopulo, A.D.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Structural basis for selective inhibition of purine nucleoside phosphorylase from Schistosoma mansoni: kinetic and structural studies.
Authors: Castilho, M.S. / Postigo, M.P. / Pereira, H.M. / Oliva, G. / Andricopulo, A.D.
History
DepositionJun 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine-nucleoside phosphorylase
B: Purine-nucleoside phosphorylase
C: Purine-nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,74211
Polymers93,5923
Non-polymers1,1508
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.577, 132.953, 121.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 3:62 or resseq 66:287 )
21chain B and (resseq 3:253 or resseq 267:287 )
31chain C and (resseq 3:287 )

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111AA3 - 623 - 62
121AA66 - 28766 - 287
211BB3 - 2533 - 253
221BB267 - 287267 - 287
311CC3 - 2873 - 287

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.965047, 0.240981, -0.103013), (0.031578, -0.497125, -0.867104), (-0.260166, 0.833544, -0.487359)1.88704, 0.846829, 15.6899
3given(0.970599, 0.025679, -0.239328), (0.221625, -0.483279, 0.846949), (-0.093914, -0.875089, -0.474762)2.17443, -13.5372, 8.44534

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Components

#1: Protein Purine-nucleoside phosphorylase


Mass: 31197.254 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: Pmal-c2G / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q9BMI9, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-BC3 / 2-amino-7-(pyridin-3-ylmethyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one / peldesine,BCX-34


Mass: 241.249 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H11N5O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 18% PEG 1500, 32mM Sodium acetate pH 4.9, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.3→89.55 Å / Num. obs: 35710 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 4.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 1.3 / Num. measured all: 19998 / Num. unique all: 5135 / Rsym value: 0.486 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.61 Å
Translation2.5 Å27.61 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.302→27.608 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.36 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 1715 5.01 %
Rwork0.201 --
obs0.204 34204 94.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.603 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 171.11 Å2 / Biso mean: 46.694 Å2 / Biso min: 9.95 Å2
Baniso -1Baniso -2Baniso -3
1-6.095 Å2-0 Å20 Å2
2---7.659 Å20 Å2
3---1.564 Å2
Refinement stepCycle: LAST / Resolution: 2.302→27.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 76 348 6754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086575
X-RAY DIFFRACTIONf_angle_d1.0638906
X-RAY DIFFRACTIONf_chiral_restr0.0691033
X-RAY DIFFRACTIONf_plane_restr0.0041137
X-RAY DIFFRACTIONf_dihedral_angle_d16.3392415
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2050X-RAY DIFFRACTIONPOSITIONAL
12B2050X-RAY DIFFRACTIONPOSITIONAL0.048
13C2149X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.302-2.3690.3231120.2272050216272
2.369-2.4460.3131110.2252585269691
2.446-2.5330.2831410.2242625276693
2.533-2.6340.3391530.2322696284995
2.634-2.7540.3051530.2162688284195
2.754-2.8990.2931570.2112739289696
2.899-3.0810.2921580.2112738289697
3.081-3.3180.3031430.2152816295998
3.318-3.6510.2651410.1962825296698
3.651-4.1780.2191420.1752892303499
4.178-5.2580.1771520.1482903305599
5.258-27.610.2271520.22932308495
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)
11.1722-0.2125-0.42741.1940.19650.5015-0.0156-0.08760.01980.2282-0.0472-0.12170.03250.00810.04290.1108-0.025-0.06370.11260.01260.0927-13.1503-15.142129.3309
21.2008-0.62210.07751.7448-0.06140.69210.0460.08550.3379-0.1607-0.1262-0.3622-0.29450.04990.06090.2194-0.00210.0180.11820.04250.2746-18.077216.0089.4857
30.8540.3637-0.20830.8411-0.20180.7864-0.0127-0.0587-0.0259-0.1899-0.0818-0.08760.0823-0.00550.0040.13570.00840.0310.09720.02410.1235-17.0753-17.9947-7.5593
40.2471-0.2125-0.19740.14770.15140.13740.07970.0354-0.04830.00070.0698-0.0885-0.0070.0939-0.00090.66620.1284-0.21870.75770.03740.36-19.19-23.44984.5873
50.06320.0486-0.04060.0727-0.03080.0218-0.0310.00840.0666-0.012-0.0293-0.02790.010.0159-0.00030.69260.16680.46360.80740.01030.6773-22.7317.6824-1.2466
60.20020.01930.1087-0.0008-0.0140.071-0.0047-0.03180.0019-0.0273-0.0775-0.073700.08330.00110.4431-0.0585-0.16020.23660.03560.6225-18.1873-2.563228.4704
71.814.36252.78512.0114-1.4123.16421.0891-3.4516-1.22145.94320.14617.82184.60674.5835-1.24380.96140.10270.290.7710.33251.0818-13.2715-7.399431.2314
82.12151.87592.02651.76532.07691.8418-0.6102-0.36551.00920.359-0.1223-3.1762-1.10092.26640.73750.73970.044-0.23360.5212-0.09710.7008-15.5626-23.2118-1.9025
94.5995-4.4361-4.73524.99117.11912.5449-1.3738-0.23192.16981.32632.5373-4.2832-0.5443-2.9138-1.14610.3360.1792-0.02350.94460.25541.1425-0.4596-15.77953.3631
1022.99346.7266222-0.67425.2721-5.16770.8242-1.25076.4563.83512.191.93960.19860.14530.09450.78220.00760.2367-3.9419-18.174514.5222
112222223.3784-5.8794.05368.3368-2.394111.43382.1618-6.7939-0.95920.5578-0.27110.17250.28020.05150.8126-5.80886.729417.6371
122.3802-5.3412.16362.3823-0.92222.33281.15883.13038.20830.97260.01918.6114-0.474-11.576-1.18030.6244-0.1420.24150.4026-0.0240.5705-7.5233-3.2239-5.2564
13-0.04620.1935-0.07460.28970.0650.18080.01740.00680.0161-0.0094-0.05110.0042-0.1155-0.00380.040.2410.0185-0.02010.2297-0.01550.2082-18.3786-8.25939.9275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L
13X-RAY DIFFRACTION13chain W

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