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- PDB-2q7o: Structure of human purine nucleoside phosphorylase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2q7o
TitleStructure of human purine nucleoside phosphorylase in complex with L-Immucillin-H
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / purine nucleoside phosphorylase
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 / PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRinaldo-Matthis, A. / Almo, S.C. / Schramm, V.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase.
Authors: Rinaldo-Matthis, A. / Murkin, A.S. / Ramagopal, U.A. / Clinch, K. / Mee, S.P. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / Almo, S.C. / Schramm, V.L.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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)32,5463
Polymers32,1851
Non-polymers3612
Water37821
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)97,6389
Polymers96,5553
Non-polymers1,0846
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 area10250 Å2
ΔGint-66 kcal/mol
Surface area30970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.457, 143.457, 166.248
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -x+y,-x,z and -y,x-y,z.

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Components

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


Mass: 32184.877 Da / Num. of mol.: 1
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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.: 21 / 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: 5.11 Å3/Da / Density % sol: 75.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.8 M Ammonium dihydrogen phosphate, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 11, 2006
RadiationMonochromator: SiIII / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. all: 14755 / Num. obs: 14741 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.073 / Χ2: 1.062 / Net I/σ(I): 7.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1442 / Rsym value: 0.73 / Χ2: 0.449 / % possible all: 99.3

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.21 Å34.54 Å
Translation3.21 Å34.54 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rr6

1rr6


Resolution: 2.9→34.54 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.764 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.434 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 745 5.1 %RANDOM
Rwork0.216 ---
all0.218 14736 --
obs0.218 14728 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.358 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.06 Å20 Å2
2--0.13 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 24 21 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0222299
X-RAY DIFFRACTIONr_angle_refined_deg2.9531.9663113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.5185283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40523.491106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.58315382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1511517
X-RAY DIFFRACTIONr_chiral_restr0.1810.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021755
X-RAY DIFFRACTIONr_nbd_refined0.3210.21260
X-RAY DIFFRACTIONr_nbtor_refined0.3540.21579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2100
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.25
X-RAY DIFFRACTIONr_mcbond_it1.2581.51448
X-RAY DIFFRACTIONr_mcangle_it2.02722259
X-RAY DIFFRACTIONr_scbond_it2.7483983
X-RAY DIFFRACTIONr_scangle_it4.2814.5854
LS refinement shellResolution: 2.904→2.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 57 -
Rwork0.321 1002 -
obs-1059 99.25 %

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