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- PDB-1pf7: CRYSTAL STRUCTURE OF HUMAN PNP COMPLEXED WITH IMMUCILLIN H -

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Basic information

Entry
Database: PDB / ID: 1pf7
TitleCRYSTAL STRUCTURE OF HUMAN PNP COMPLEXED WITH IMMUCILLIN H
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 / 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-IMH / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDe Azevedo Jr., W.F. / Canduri, F. / Dos Santos, D.M. / Pereira, J.H. / Dias, M.V.B. / Silva, R.G. / Mendes, M.A. / Palma, M.S. / Basso, L.A. / Santos, D.S.
Citation
History
DepositionMay 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Oct 5, 2022Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.pdbx_synonyms / _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
Revision 2.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
E: PURINE NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7395
Polymers32,1851
Non-polymers5544
Water1,15364
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)98,21815
Polymers96,5553
Non-polymers1,66312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10830 Å2
ΔGint-171 kcal/mol
Surface area29200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)139.390, 139.390, 161.310
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 / E.C.2.4.2.1 / INOSINE PHOSPHORYLASE / PNP


Mass: 32184.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: complexed with IMMUCILLIN H, residue IMH / Source: (gene. exp.) Homo sapiens (human) / 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-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H


Mass: 266.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N4O4 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 4.92 Å3/Da / Density % sol: 75 %
Crystal growpH: 5.3
Details: 0.05M CITRATE BUFFER, 19% AMMONIUM SULPHATE, pH 5.30

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.431
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 16, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.431 Å / Relative weight: 1
ReflectionResolution: 2.6→56.531 Å / Num. obs: 16763 / % possible obs: 90.1 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rsym value: 0.099 / Net I/σ(I): 6.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.375 / % possible all: 93.4

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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: 1M73

1m73


Resolution: 2.6→7 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1538 10 %RANDOM
Rwork0.2 ---
obs0.2 15383 89.8 %-
all-16705 --
Displacement parametersBiso mean: 28.91 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 34 64 2349
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.893
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.82
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.59
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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