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- PDB-1rfg: Crystal Structure of Human Purine Nucleoside Phosphorylase Comple... -

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Basic information

Entry
Database: PDB / ID: 1rfg
TitleCrystal Structure of Human Purine Nucleoside Phosphorylase Complexed with Guanosine
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE / DRUG DESIGN / SYNCHROTRON / GUANOSINE
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 / 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
GUANOSINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCanduri, F. / Silva, R.G. / Dos Santos, D.M. / Palma, M.S. / Basso, L.A. / Santos, D.S. / de Azevedo, W.F.
Citation
#1: Journal: BIOCHEM.BIOPHYS.RES.COMMUN. / Year: 2003
Title: Crystal Structural of Human Purine Nucleoside Phosphorylase at 2.3 Angstrom Resolution
Authors: de Azevedo Jr., W.F. / Canduri, F. / dos Santos, D.M. / Silva, R.G. / de Oliveira, J.S. / de Carvalho, L.P. / Basso, L.A. / Mendes, M.A. / Palma, M.S. / Santos, D.S.
History
DepositionNov 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
E: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6255
Polymers32,0541
Non-polymers5714
Water30617
1
E: Purine nucleoside phosphorylase
hetero molecules

E: Purine nucleoside phosphorylase
hetero molecules

E: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,87515
Polymers96,1613
Non-polymers1,71412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area11420 Å2
ΔGint-178 kcal/mol
Surface area28960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)139.380, 139.380, 160.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 32053.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP / Plasmid: PET-23A+ / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.68 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: AMMONIUM SULFATE, pH 5.30, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
ReflectionResolution: 2.9→48.224 Å / Num. obs: 14265 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 2.9→3.01 Å / Rmerge(I) obs: 0.214 / % possible all: 97.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PWY

1pwy


Resolution: 2.9→7 Å / Data cutoff high absF: 2 / Data cutoff low absF: 2 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1056 10 %RANDOM
Rwork0.206 ---
obs0.206 10650 48.224 %-
all-14194 --
Displacement parametersBiso mean: 33.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.3337 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 35 17 2303
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg2.003
X-RAY DIFFRACTIONx_dihedral_angle_d25.21
X-RAY DIFFRACTIONx_improper_angle_d1.79
LS refinement shellHighest resolution: 2.9 Å
RfactorNum. reflection% reflection
Rfree0.262 1056 -
Rwork0.202 --
obs-13138 96.5 %

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