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

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Basic information

Entry
Database: PDB / ID: 4ece
TitleCrystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with guanine
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / PNP / guanine / Purine nucleoside phosphorylase / nucleoside binding / purine base binding / purine-nucleoside phosphorylase activity / drug binding / transferring glycosyl groups / phosphate ion binding / intracellular / cytosol
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 / nucleotide biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine 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 / nucleotide biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inosine catabolic process / urate biosynthetic process / IMP catabolic process / Ribavirin ADME / guanosine phosphorylase activity / nucleoside binding / Purine salvage / Purine catabolism / allantoin metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / positive regulation of alpha-beta T cell differentiation / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / 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 / 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
GUANINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 26, 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
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,67012
Polymers216,7636
Non-polymers9076
Water5,495305
1
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8356
Polymers108,3813
Non-polymers4533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-21 kcal/mol
Surface area32450 Å2
MethodPISA
2
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8356
Polymers108,3813
Non-polymers4533
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-21 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.553, 129.676, 104.346
Angle α, β, γ (deg.)90.00, 105.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.250566, -0.074923, 0.965196), (-0.878394, 0.436734, -0.19413), (-0.406989, -0.896465, -0.175243)-19.15956, -24.93316, -26.0279
3given(-0.249367, -0.872667, -0.419844), (-0.0807, 0.450758, -0.888991), (0.965041, -0.187804, -0.182828)-36.99704, -13.39441, 9.24237
4given(-0.765926, 0.595478, 0.24241), (-0.612865, -0.790174, 0.004631), (0.194304, -0.145018, 0.970163)-10.73059, -18.3784, 52.54174
5given(0.418835, -0.226828, 0.879276), (0.341015, -0.858135, -0.383813), (0.841598, 0.4606, -0.282065)35.82217, -32.89026, -13.96942
6given(0.648641, 0.597767, -0.471105), (-0.393861, -0.266022, -0.879833), (-0.65126, 0.756245, 0.062884)-40.29243, -67.63328, -7.0838

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Components

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


Mass: 36127.129 Da / Num. of mol.: 6 / 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-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H5N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16% PEG 8000, 20% glycerol, 0.16M magnesium acetate, 0.08M sodium cacodylate, pH 6.5, 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: Dec 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 61417 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 26.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2 / Num. unique all: 6104 / Rsym value: 0.872 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.04 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.235 / SU ML: 0.258 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.158 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26099 3106 5.1 %RANDOM
Rwork0.22152 ---
obs0.22346 58023 99.93 %-
all-53481 --
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: 73.321 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.58 Å2
2--2.77 Å20 Å2
3----2.84 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13234 0 66 305 13605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913639
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.351.96918464
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7851700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10523.365627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.834152270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.21215103
X-RAY DIFFRACTIONr_chiral_restr0.0860.21994
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110491
X-RAY DIFFRACTIONr_gen_planes_other
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: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 227 -
Rwork0.367 4238 -
obs--99.75 %

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