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

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Basic information

Entry
Database: PDB / ID: 4gka
TitleCrystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with phosphate
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / purine nucleoside phosphorylase / nucleoside binding / purine base binding / purine-nucleoside phosphorylase activity / drug binding / transferase activity / 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 / 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
PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionAug 10, 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 1.3Dec 21, 2022Group: 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)217,51714
Polymers216,7636
Non-polymers7548
Water7,278404
1
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7587
Polymers108,3813
Non-polymers3774
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-55 kcal/mol
Surface area30540 Å2
MethodPISA
2
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7587
Polymers108,3813
Non-polymers3774
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-56 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.882, 233.670, 70.077
Angle α, β, γ (deg.)90.00, 97.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.965023, -0.067076, 0.253438), (-0.07203, -0.997349, 0.01031), (0.252075, -0.028204, -0.967297)-13.97829, 63.52233, 28.19473

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Components

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


Mass: 36127.129 Da / Num. of mol.: 6 / Fragment: NONE / 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-TOP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.02 Å3/Da / Density % sol: 39.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M zinc acetate, 10% (v/v) 2-propanol, 0.1M 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: Apr 12, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochrometer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 86349 / Num. obs: 86349 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 19.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8627 / Rsym value: 0.876 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.29 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.893 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.28 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23204 4320 5 %RANDOM
Rwork0.18798 ---
all0.19023 86296 --
obs0.19023 81976 99.56 %-
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: 47.737 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å2-0 Å2-0.69 Å2
2---0.84 Å2-0 Å2
3----3.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12575 0 42 404 13021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912971
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212389
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.96717548
X-RAY DIFFRACTIONr_angle_other_deg0.801328415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06751616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94822.98604
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.211152162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.78315110
X-RAY DIFFRACTIONr_chiral_restr0.070.21903
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114770
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023132
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 297 -
Rwork0.315 5794 -
obs-6091 94.79 %

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