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- PDB-3ggs: Human purine nucleoside phosphorylase double mutant E201Q,N243D c... -

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Basic information

Entry
Database: PDB / ID: 3ggs
TitleHuman purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoro-2'-deoxyadenosine
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / enzyme-prodrug complex / Disease mutation / Glycosyltransferase
Function / homology
Function and homology information


nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / nucleotide biosynthetic process / dAMP catabolic process / urate biosynthetic process ...nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / nucleotide biosynthetic process / dAMP catabolic process / urate biosynthetic process / Ribavirin ADME / IMP catabolic process / nucleoside binding / guanosine phosphorylase activity / Purine catabolism / allantoin metabolic process / Purine salvage / purine-nucleoside phosphorylase / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / purine-nucleoside phosphorylase activity / positive regulation of alpha-beta T cell differentiation / phosphate ion binding / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / secretory granule lumen / ficolin-1-rich granule lumen / response to xenobiotic stimulus / immune response / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / 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-2FD / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.52 Å
AuthorsSawaya, M.R. / Afshar, S.
CitationJournal: Protein Sci. / Year: 2009
Title: Structure of a mutant human purine nucleoside phosphorylase with the prodrug, 2-fluoro-2'-deoxyadenosine and the cytotoxic drug, 2-fluoroadenine.
Authors: Afshar, S. / Sawaya, M.R. / Morrison, S.L.
History
DepositionMar 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)107,16037
Polymers103,2013
Non-polymers3,95934
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-32 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.240, 130.646, 149.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Purine nucleoside phosphorylase / PNP / Inosine phosphorylase


Mass: 34400.246 Da / Num. of mol.: 3 / Mutation: E201Q, N243D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-2FD / 5-(6-AMINO-2-FLUORO-PURIN-9-YL)-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-OL / 2-FLUORO-2'-DEOXYADENOSINE


Mass: 269.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12FN5O3
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.54M Ammonium sulfate, 0.05M Sodium potassium phosphate pH 6.8, 3% Trimethylamine N-oxide, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 47561 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 57.2 Å2 / Rmerge(I) obs: 0.09 / Χ2: 0.935 / Net I/σ(I): 17.887
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.39 / Num. unique all: 4622 / Χ2: 0.977 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
REFMAC5.4.0061phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3GB9

3gb9


Resolution: 2.52→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.225 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.784 / SU B: 21.198 / SU ML: 0.216 / SU R Cruickshank DPI: 0.34 / SU Rfree: 0.253 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2395 5 %RANDOM
Rwork0.212 ---
obs0.214 47486 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.26 Å2 / Biso mean: 52.026 Å2 / Biso min: 24.21 Å2
Baniso -1Baniso -2Baniso -3
1-8.33 Å20 Å20 Å2
2---3.53 Å20 Å2
3----4.81 Å2
Refinement stepCycle: LAST / Resolution: 2.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6614 0 226 64 6904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226969
X-RAY DIFFRACTIONr_bond_other_d0.0010.024681
X-RAY DIFFRACTIONr_angle_refined_deg1.261.9919457
X-RAY DIFFRACTIONr_angle_other_deg0.88311349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72123.462312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.394151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4661551
X-RAY DIFFRACTIONr_chiral_restr0.070.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021444
X-RAY DIFFRACTIONr_mcbond_it1.40224197
X-RAY DIFFRACTIONr_mcbond_other0.37321732
X-RAY DIFFRACTIONr_mcangle_it2.38136737
X-RAY DIFFRACTIONr_scbond_it1.44422772
X-RAY DIFFRACTIONr_scangle_it2.09132720
LS refinement shellResolution: 2.52→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 153 -
Rwork0.321 2899 -
all-3052 -
obs--87.08 %
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)
11.0704-0.4973-0.18380.92830.78853.4399-0.0277-0.1213-0.0334-0.26350.00090.17290.3978-0.18070.0268-0.1231-0.0188-0.0417-0.12610.0247-0.132-14.69186.0883-54.9627
21.69861.2824-0.45933.10520.0851.12420.06720.1360.0883-0.0420.04760.1702-0.3718-0.078-0.11480.11130.03070.0128-0.15640.0052-0.1597-10.583738.4047-37.5186
31.3288-0.3922-0.47511.6007-0.58872.0459-0.074-0.11440.08990.22180.0247-0.0785-0.11270.00080.04930.1004-0.0268-0.0166-0.1543-0.0092-0.1696-15.13437.4463-17.7967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 286
2X-RAY DIFFRACTION2B3 - 285
3X-RAY DIFFRACTION3C3 - 285

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