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- PDB-3e9z: Crystal structure of purine nucleoside phosphorylase from Schisto... -

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Basic information

Entry
Database: PDB / ID: 3e9z
TitleCrystal structure of purine nucleoside phosphorylase from Schistosoma mansoni in complex with 6-chloroguanine
ComponentsPurine-nucleoside phosphorylase
KeywordsTRANSFERASE / Schistosoma Purine Nucleoside Phosphorylase / Glycosyltransferase
Function / homology
Function and homology information


nucleoside metabolic process / guanosine 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-chloroguanine / ACETATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.31 Å
AuthorsPereira, H.M. / Rezende, M.M. / Oliva, G. / Garratt, R.C.
CitationJournal: To be Published
Title: Crystal structure of Schistosoma mansoni purine nucleoside phosphorylase (SmPNP) in complex with adenine, 8-aminoguanine, 8-azaguanine and 6-chloroguanine.
Authors: Pereira, H.M. / Rezende, M.M. / Oliva, G. / Garratt, R.C.
History
DepositionAug 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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)94,59113
Polymers93,5923
Non-polymers99910
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-50 kcal/mol
Surface area29120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.821, 118.121, 129.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain A and (resseq 5:34 or resseq 38:61 or resseq 67:252 or resseq 269:287 )
21chain B and (resseq 5:34 or resseq 38:61 or resseq 67:252 or resseq 269:287 )
31chain C and (resseq 5:34 or resseq 38:61 or resseq 67:252 or resseq 269:287 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLYGLYAA5 - 345 - 34
12GLYGLYTHRTHRAA38 - 6138 - 61
13SERSERGLUGLUAA67 - 25267 - 252
14ARGARGASPASPAA269 - 287269 - 287
21VALVALGLYGLYBB5 - 345 - 34
22GLYGLYTHRTHRBB38 - 6138 - 61
23SERSERGLUGLUBB67 - 25267 - 252
24ARGARGASPASPBB269 - 287269 - 287
31VALVALGLYGLYCC5 - 345 - 34
32GLYGLYTHRTHRCC38 - 6138 - 61
33SERSERGLUGLUCC67 - 25267 - 252
34ARGARGLYSLYSCC269 - 286269 - 286

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Components

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Protein , 1 types, 3 molecules ABC

#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) / Gene: SmPNP / Plasmid: pMAL-C2G / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q9BMI9, purine-nucleoside phosphorylase

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Non-polymers , 5 types, 690 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-6GU / 6-chloroguanine / 6-chloro-9H-purin-2-amine


Mass: 169.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4ClN5
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 18-20% PEG 1500, 20% Glycerol, 32mM Sodium acetate, VAPOR DIFFUSION, temperature 277K
PH range: 4.9-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 2.3→129.05 Å / Num. obs: 30649 / % possible obs: 95.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 7.93
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.422.70.4181.61120341280.41890.3
2.42-2.572.80.3122.31123440380.31292.7
2.57-2.752.90.223.21117738590.2294.3
2.75-2.973.10.1574.51135136560.15796
2.97-3.253.30.1086.71159934690.10897.8
3.25-3.643.50.0739.81117431640.07398
3.64-4.23.60.05312.81028728610.05399.2
4.2-5.143.60.04713.6875624330.04799
5.14-7.273.60.0611.6679219130.0699
7.27-129.053.30.04313.8369511280.04398.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1TD1

1td1


Resolution: 2.31→56.629 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.249 1480 5.04 %
Rwork0.177 --
obs0.18 29343 90.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.759 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 179.31 Å2 / Biso mean: 27.4 Å2 / Biso min: 8.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.628 Å2-0 Å20 Å2
2---2.653 Å20 Å2
3---0.025 Å2
Refinement stepCycle: LAST / Resolution: 2.31→56.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 57 680 7055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096484
X-RAY DIFFRACTIONf_angle_d1.2678779
X-RAY DIFFRACTIONf_chiral_restr0.0931026
X-RAY DIFFRACTIONf_plane_restr0.0061122
X-RAY DIFFRACTIONf_dihedral_angle_d16.6492354
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1978X-RAY DIFFRACTIONPOSITIONAL
12B1978X-RAY DIFFRACTIONPOSITIONAL0.071
13C1970X-RAY DIFFRACTIONPOSITIONAL0.061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.3850.294980.222111220977
2.385-2.470.2931210.2072245236682
2.47-2.5690.2971230.1882348247186
2.569-2.6860.251210.1842449257089
2.686-2.8270.2611280.1792465259389
2.827-3.0050.3091640.1762512267692
3.005-3.2370.2371390.1652647278696
3.237-3.5620.2171430.1512700284396
3.562-4.0770.231340.1372736287098
4.077-5.1370.1921740.142754292898
5.137-56.6460.251350.1962896303197

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