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- PDB-1vfn: PURINE NUCLEOSIDE PHOSPHORYLASE -

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Basic information

Entry
Database: PDB / ID: 1vfn
TitlePURINE NUCLEOSIDE PHOSPHORYLASE
ComponentsPURINE-NUCLEOSIDE PHOSPHORYLASE
KeywordsNUCLEOSIDE PHOSPHORYLASE / TRANSFERASE / GLYCOSYLTRANSFERASE / DISEASE MUTATION
Function / homology
Function and homology information


guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / 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
HYPOXANTHINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKoellner, G. / Bzowska, A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 A resolution.
Authors: Koellner, G. / Luic, M. / Shugar, D. / Saenger, W. / Bzowska, A.
#1: Journal: FEBS Lett. / Year: 1995
Title: Calf Spleen Purine Nucleoside Phosphorylase: Purification, Sequence and Crystal Structure of its Complex with an N(7)-Acycloguanosine Inhibitor
Authors: Bzowska, A. / Luic, M. / Schroder, W. / Shugar, D. / Saenger, W. / Koellner, G.
History
DepositionOct 8, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PURINE-NUCLEOSIDE PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5394
Polymers31,3131
Non-polymers2263
Water2,324129
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)94,61612
Polymers93,9383
Non-polymers6779
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z+1/2,-x+3/2,-y+11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area8260 Å2
ΔGint-46 kcal/mol
Surface area29910 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)94,61612
Polymers93,9383
Non-polymers6779
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Buried area3100 Å2
ΔGint-64 kcal/mol
Surface area35170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.110, 94.110, 94.110
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-434-

ZN

21A-432-

HOH

31A-433-

HOH

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Components

#1: Protein PURINE-NUCLEOSIDE PHOSPHORYLASE


Mass: 31312.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: SPLEEN
References: UniProt: P55859, purine-nucleoside phosphorylase
#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-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.22 Å3/Da / Density % sol: 43 %
Crystal growpH: 8
Details: 16%(W/V) PEG 4000, 0.04M TRIS-HCL BUFFER PH 8.2-8.5, 0.08M MGCL2, pH 8.0
PH range: 8.2-8.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.6-8 mg/mlPNP-hypoxanthine1drop
26.6 mMsodium citrate1drop
30.6 mMbeta-mercaptoethanol1drop
43.6-5.3 %(w/v)PEG40001drop
50.01 MTris-HCl1drop
60.03 M1dropMgCl2
711-16 %(w/v)PEG40001reservoir
80.04 MTris-HCl1reservoir
90.08 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9204
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9204 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 15158 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 3.27 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6 / % possible all: 97.6

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ULB

1ulb


Resolution: 2.15→20 Å / Isotropic thermal model: TNT PACKAGE / σ(F): 1 / Stereochemistry target values: TNT PACKAGE
RfactorNum. reflection% reflection
Rwork0.18 --
obs-15158 98.4 %
Solvent computationSolvent model: TNT PACKAGE / Bsol: 173 Å2 / ksol: 0.665 e/Å3
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 12 129 2243
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0221570.02
X-RAY DIFFRACTIONt_angle_deg2.829013
X-RAY DIFFRACTIONt_dihedral_angle_d26.1127730
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005530.02
X-RAY DIFFRACTIONt_gen_planes0.0113170.02
X-RAY DIFFRACTIONt_it3.8582146
X-RAY DIFFRACTIONt_nbd0.02640
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0050.02
X-RAY DIFFRACTIONt_plane_restr0.0110.02

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