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- PDB-1rct: Crystal structure of Human purine nucleoside phosphorylase comple... -

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Basic information

Entry
Database: PDB / ID: 1rct
TitleCrystal structure of Human purine nucleoside phosphorylase complexed with INOSINE
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / purine nucleoside phosphorylase / drug design / Synchrotron
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 / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / 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
INOSINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCanduri, F. / dos Santos, D.M. / Silva, R.G. / Mendes, M.A. / Palma, M.S. / de Azevedo Jr., W.F. / Basso, L.A. / Santos, D.S.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Structures of human purine nucleoside phosphorylase complexed with inosine and ddI
Authors: Canduri, F. / dos Santos, D.M. / Silva, R.G. / Mendes, M.A. / Basso, L.A. / Palma, M.S. / de Azevedo Jr., W.F. / Santos, D.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors
Authors: Ealick, S.E. / Babu, Y.S. / Bugg, C.E. / Erion, M.D. / Guida, W.C. / Montgomery, J.A. / Secrist III, J.A.
History
DepositionNov 4, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
E: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6105
Polymers32,0541
Non-polymers5564
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)97,83015
Polymers96,1613
Non-polymers1,66912
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 area10790 Å2
ΔGint-179 kcal/mol
Surface area30070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.990, 140.990, 161.130
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) / Plasmid: PET-23A+ / Production host: Escherichia coli (E. coli)
References: UniProt: P00491, purine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NOS / INOSINE / Inosine


Mass: 268.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N4O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.825 Å3/Da / Density % sol: 71 %
Crystal growpH: 5.3 / Details: pH 5.30
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
210 mMpotassium phosphate1droppH7.1
319 %(v/v)satammonium sulfate1reservoir
40.05 Mcitrate1reservoirpH5.3

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431 / Wavelength: 1.431 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 19, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4311
21.4311
ReflectionResolution: 2.8→56.79 Å / Num. all: 109144 / Num. obs: 15363 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.216 / % possible all: 95.7
Reflection
*PLUS
Redundancy: 5.5 %
Reflection shell
*PLUS
% possible obs: 95.7 % / Rmerge(I) obs: 0.268

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Processing

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

1pwy


Resolution: 2.8→8 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
Rfree0.29 1443 10 %RANDOM
Rwork0.208 ---
all0.213 15363 --
obs0.208 15363 99.99 %-
Displacement parametersBiso mean: 43.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 34 45 2330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d25.25
X-RAY DIFFRACTIONx_improper_angle_d1.7
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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