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- PDB-2a0y: Structure of human purine nucleoside phosphorylase H257D mutant -

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Basic information

Entry
Database: PDB / ID: 2a0y
TitleStructure of human purine nucleoside phosphorylase H257D mutant
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / purine nucleoside phosphorylase / transition state inhibitor / mutant
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 / Ribavirin ADME / IMP catabolic process / nucleoside binding / guanosine phosphorylase activity / Purine catabolism / allantoin metabolic process / Purine salvage / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / 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-DIH / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 Å
AuthorsMurkin, A.S. / Shi, W. / Schramm, V.L.
CitationJournal: Biochemistry / Year: 2007
Title: Neighboring group participation in the transition state of human purine nucleoside phosphorylase.
Authors: Murkin, A.S. / Birck, M.R. / Rinaldo-Matthis, A. / Shi, W. / Taylor, E.A. / Almo, S.C. / Schramm, V.L.
History
DepositionJun 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Dec 12, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Oct 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 2.2Aug 23, 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

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6194
Polymers32,1621
Non-polymers4573
Water82946
1
A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,85812
Polymers96,4853
Non-polymers1,3729
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10970 Å2
ΔGint-124 kcal/mol
Surface area30380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.467, 142.467, 166.029
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the crystallographic 3-fold

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Components

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


Mass: 32161.818 Da / Num. of mol.: 1 / Mutation: H257D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP / Production host: Escherichia coli (E. coli)
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DIH / 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one


Mass: 265.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 4.7 Å3/Da / Density % sol: 76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Na citrate, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. all: 29445 / Num. obs: 29445 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 41.9 Å2 / Rsym value: 0.051 / Net I/σ(I): 43.6
Reflection shellResolution: 2.28→2.36 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 2907 / Rsym value: 0.564 / % possible all: 99.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1RSZ

1rsz


Resolution: 2.28→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2804 -random
Rwork0.243 ---
all0.245 28222 --
obs0.245 28222 95 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.42 Å26.72 Å20 Å2
2--2.42 Å20 Å2
3----4.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.28→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 29 46 2279
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.28→2.42 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.337 350 -
Rwork0.304 --
obs-3046 69.1 %

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