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- PDB-1fxu: PURINE NUCLEOSIDE PHOSPHORYLASE FROM CALF SPLEEN IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 1fxu
TitlePURINE NUCLEOSIDE PHOSPHORYLASE FROM CALF SPLEEN IN COMPLEX WITH N(7)-ACYCLOGUANOSINE INHIBITOR AND A PHOSPHATE ION
ComponentsPURINE NUCLEOSIDE PHOSPHORYLASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / NUCLEOSIDE PHOSPHORYLASE
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
Chem-GU7 / PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsLuic, M. / Bzowska, A. / Shugar, D. / Saenger, W. / Koellner, G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Calf spleen purine nucleoside phosphorylase: structure of its ternary complex with an N(7)-acycloguanosine inhibitor and a phosphate anion.
Authors: Luic, M. / Koellner, G. / Shugar, D. / Saenger, W. / Bzowska, A.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Crystals 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.
History
DepositionSep 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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

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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)32,5175
Polymers32,0641
Non-polymers4534
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)97,55215
Polymers96,1933
Non-polymers1,35912
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 area9650 Å2
ΔGint-92 kcal/mol
Surface area28890 Å2
MethodPISA, PQS
3
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)97,55215
Polymers96,1933
Non-polymers1,35912
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 area4430 Å2
ΔGint-98 kcal/mol
Surface area34210 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-302-

ZN

21A-364-

HOH

31A-371-

HOH

41A-372-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PURINE NUCLEOSIDE PHOSPHORYLASE /


Mass: 32064.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: SPLEEN
References: UniProt: P55859, purine-nucleoside phosphorylase

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Non-polymers , 5 types, 117 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GU7 / 2-AMINO-7-[2-(2-HYDROXY-1-HYDROXYMETHYL-ETHYLAMINO)-ETHYL]-1,7-DIHYDRO-PURIN-6-ONE


Mass: 268.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.04M Tris/HCl buffer, PEG 4000, 11-16%, 0.08M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
pH: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-12 mg/mlprotein1drop
210 mMsodium citrate1drop
31 mMbeta-mercaptoethanol1drop
511-16 %(v/v)PEG40001reservoir
60.04 MTris-HCl1reservoir
70.08 M1reservoirMgCl2
4reservoir solution1drop

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Data collection

DiffractionMean temperature: 4 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.908
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 6, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.2→22.2 Å / Num. all: 12786 / Num. obs: 12786 / Observed criterion σ(F): 2893461.04 / Biso Wilson estimate: 12.5 Å2
Reflection
*PLUS
% possible obs: 89 % / Num. measured all: 38538 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 87.2 %

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.2→22.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2893461.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1320 10.3 %RANDOM
Rwork0.175 ---
obs0.175 12786 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.19 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→22.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 26 113 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it3.272
X-RAY DIFFRACTIONc_scangle_it4.392.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 219 10.6 %
Rwork0.214 1850 -
obs--87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE2.PARAMPROTEIN.LINK
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4GU7.PARGU7.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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