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- PDB-2oc4: Crystal structure of human purine nucleoside phosphorylase mutant... -

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Basic information

Entry
Database: PDB / ID: 2oc4
TitleCrystal structure of human purine nucleoside phosphorylase mutant H257D with Imm-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 / 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 / cytoplasm / cytosol
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: 2.592 Å
AuthorsRinaldo-Matthis, A. / Almo, S.C. / 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
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Oct 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 2.0Oct 5, 2022Group: Atomic model / Structure summary / Category: atom_site / chem_comp
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
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:
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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5233
Polymers32,1621
Non-polymers3612
Water86548
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)97,5699
Polymers96,4853
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 area10210 Å2
ΔGint-48 kcal/mol
Surface area31540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.974, 142.974, 168.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-544-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase / E.C.2.4.2.1 / Inosine phosphorylase / PNP


Mass: 32161.818 Da / Num. of mol.: 1 / Fragment: purine nucleoside phosphorylase / 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-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium Acetate, 4.0 M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.592→30 Å / Num. all: 20698 / Num. obs: 20554 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.071 / Χ2: 0.675 / Net I/σ(I): 7.1
Reflection shellResolution: 2.592→2.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1945 / Rsym value: 0.62 / Χ2: 0.383 / % possible all: 94.6

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Phasing

Phasing MRRfactor: 0.378 / Cor.coef. Fo:Fc: 0.749
Highest resolutionLowest resolution
Rotation3 Å29.6 Å
Translation3 Å29.6 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RR6

1rr6


Resolution: 2.592→29.06 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.945 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.257 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1051 5.1 %RANDOM
Rwork0.205 ---
all0.207 20731 --
obs0.207 20551 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.592→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 24 48 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222312
X-RAY DIFFRACTIONr_angle_refined_deg2.2191.973132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4575285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29523.645107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.19615383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7281517
X-RAY DIFFRACTIONr_chiral_restr0.1290.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021769
X-RAY DIFFRACTIONr_nbd_refined0.3350.21132
X-RAY DIFFRACTIONr_nbtor_refined0.360.21585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.27
X-RAY DIFFRACTIONr_mcbond_it1.87821438
X-RAY DIFFRACTIONr_mcangle_it3.15832278
X-RAY DIFFRACTIONr_scbond_it1.6612975
X-RAY DIFFRACTIONr_scangle_it2.5463854
LS refinement shellResolution: 2.592→2.659 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 70 -
Rwork0.32 1273 -
obs-1343 90.5 %

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