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- PDB-4ear: Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y,... -

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Basic information

Entry
Database: PDB / ID: 4ear
TitleCrystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with DADMe-ImmG and phosphate
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PNP / Immucillin / Purine nucleoside phosphorylase / nucleoside binding / purine base binding / purine-nucleoside phosphorylase activity / drug binding / transferase activity / transferring glycosyl groups / phosphate ion binding / cytosol / 6-FLUORO-L-TRYPTOPHAN / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / dAMP catabolic process / nucleotide biosynthetic 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 / dAMP catabolic process / nucleotide biosynthetic process / urate biosynthetic process / Ribavirin ADME / IMP catabolic process / nucleoside binding / guanosine phosphorylase activity / Purine catabolism / allantoin metabolic process / Purine salvage / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / nucleobase-containing compound metabolic process / 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 / immune response / response to xenobiotic stimulus / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm
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-IM5 / PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHaapalainen, A.M. / Ho, M.C. / Suarez, J.J. / Almo, S.C. / Schramm, V.L.
CitationJournal: Chem.Biol. / Year: 2013
Title: Catalytic Site Conformations in Human PNP by (19)F-NMR and Crystallography.
Authors: Suarez, J. / Haapalainen, A.M. / Cahill, S.M. / Ho, M.C. / Yan, F. / Almo, S.C. / Schramm, V.L.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Mar 13, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)109,5589
Polymers108,4353
Non-polymers1,1236
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-61 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.916, 131.100, 137.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36145.117 Da / Num. of mol.: 3 / Mutation: W16Y, W94Y, W178Y, H257W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP, X00737.1 / Plasmid: pCRT7/NT-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical ChemComp-IM5 / 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one / DADMe-ImmG


Mass: 279.295 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H17N5O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 1000, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2011
Details: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 113686 / Num. obs: 110270 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 47.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 8 % / Rmerge(I) obs: 0.914 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5375 / Rsym value: 0.914 / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.24 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.954 / SU ML: 0.087 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20293 5592 5.1 %RANDOM
Rwork0.17465 ---
obs0.17609 104515 98.27 %-
all-97167 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.67 Å2
Baniso -1Baniso -2Baniso -3
1-4.84 Å20 Å20 Å2
2---2.77 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6681 0 75 574 7330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196995
X-RAY DIFFRACTIONr_bond_other_d0.0030.026647
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9869492
X-RAY DIFFRACTIONr_angle_other_deg0.8883.00415282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.923.292319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.871151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4451556
X-RAY DIFFRACTIONr_chiral_restr0.080.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217987
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021668
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 421 -
Rwork0.349 7552 -
obs--97.29 %

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