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- PDB-2ai2: Purine nucleoside phosphorylase from calf spleen -

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Basic information

Entry
Database: PDB / ID: 2ai2
TitlePurine nucleoside phosphorylase from calf spleen
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / purine nucleoside phosphorylase / multisubstrate analog inhibitor
Function / homology
Function and homology information


guanosine catabolic process / deoxyinosine catabolic process / deoxyguanosine catabolic process / inosine catabolic process / guanosine phosphorylase activity / NAD+ biosynthetic process via the salvage pathway / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / cytosol
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Chem-P1D / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsToms, A.V. / Wang, W. / Li, Y. / Ganem, B. / Ealick, S.E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Novel multisubstrate inhibitors of mammalian purine nucleoside phosphorylase.
Authors: Toms, A.V. / Wang, W. / Li, Y. / Ganem, B. / Ealick, S.E.
#1: Journal: Biochemistry / Year: 1998
Title: Calf Spleen Purine Nucleoside Phosphorylase Complexed with Substrates and Substrate Analogs.
Authors: Mao, C. / Cook, W.J. / Zhou, M. / Fedorov, A.A. / Almo, S.C. / Ealick, S.E.
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7135
Polymers32,1281
Non-polymers5854
Water4,648258
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)98,13815
Polymers96,3833
Non-polymers1,75512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_656-z+3/2,-x,y+3/21
crystal symmetry operation10_536-y,z-3/2,-x+3/21
Buried area9410 Å2
ΔGint-37 kcal/mol
Surface area29620 Å2
MethodPISA, PQS
2
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)98,13815
Polymers96,3833
Non-polymers1,75512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area6010 Å2
ΔGint-258 kcal/mol
Surface area33310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.243, 93.243, 93.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-291-

ZN

21A-292-

144

31A-292-

144

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit.

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 32127.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: calf spleen purine nucleoside phosphorylase purchased from Sigma Co.
Source: (natural) Bos taurus (domestic cattle) / Organ: spleen
References: UniProt: P55859, purine-nucleoside phosphorylase

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#5: Chemical ChemComp-P1D / ((2S,3AS,4R,6S)-4-(HYDROXYMETHYL)-6-(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-TETRAHYDROFURO[3,4-D][1,3]DIOXO L-2-YL)METHYLPHOSPHONIC ACID / 9-DEAZAINOSINE-2',3'-O-ETHYLIDENEPHOSPHONATE


Mass: 373.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N3O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.1 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG2K MME , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9231 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9231 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 29947 / Num. obs: 28798 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.055 / Net I/σ(I): 23.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 2970 / Rsym value: 0.439 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1A9P

1a9p


Resolution: 1.7→38.07 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 485117.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1416 4.9 %RANDOM
Rwork0.196 ---
all0.198 29947 --
obs0.196 28798 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.3003 Å2 / ksol: 0.381973 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 35 258 2409
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 230 5.2 %
Rwork0.219 4203 -
obs--89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4tris.paramtris.top
X-RAY DIFFRACTION5p1d.paramp1d.top

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