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- PDB-1lvu: Crystal structure of calf spleen purine nucleoside phosphorylase ... -

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Basic information

Entry
Database: PDB / ID: 1lvu
TitleCrystal structure of calf spleen purine nucleoside phosphorylase in a new space group with full trimer in the asymmetric unit
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / PNP / PURIE NUCLEOSIDE PHOSPHORYLASE / PENTOSYLTRANSFERASE / NEW SPACE GROUP / 2 / 6-DIAMINOPURINE MULTISUBSTRATE ANALOGUE INHIBITOR
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-9PP / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBzowska, A. / Koellner, G. / Wielgus-Kutrowska, B. / Stroh, A. / Raszewski, G. / Holy, A. / Steiner, T. / Frank, J.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of calf spleen purine nucleoside phosphorylase with two full trimers in the asymmetric unit: important implications for the mechanism of catalysis
Authors: Bzowska, A. / Koellner, G. / Wielgus-Kutrowska, B. / Stroh, A. / Raszewski, G. / Holy, A. / Steiner, T. / Frank, J.
#1: Journal: NUCLEOSIDES NUCLEOTIDES NUCLEIC ACIDS / Year: 2003
Title: Crystal Structure of Calf Spleen Purine Nucleoside in a Complex with Multisubstrate Analogue Inhibitor with 2,6-Diaminopurine Aglycone
Authors: Koellner, G. / Stroh, A. / Raszewski, G. / Holy, A. / Bzowska, A.
#2: 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.
#3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2001
Title: Calf Spleen Purine Nucleoside Phsophorylase: Crystal 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.
History
DepositionMay 29, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 4, 2018Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _software.version
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_id / _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

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
D: Purine nucleoside phosphorylase
E: Purine nucleoside phosphorylase
F: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,96122
Polymers192,7596
Non-polymers2,20216
Water32,9491829
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19850 Å2
ΔGint-200 kcal/mol
Surface area58270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.014, 132.625, 177.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo biologicaly active trimers (forming hexamer) are present in one asymmetric unit.

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Components

#1: Protein
Purine nucleoside phosphorylase


Mass: 32126.557 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: spleen
References: UniProt: P55859, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-9PP / 2,6-DIAMINO-(S)-9-[2-(PHOSPHONOMETHOXY)PROPYL]PURINE


Mass: 300.211 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H13N6O4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1829 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: PEG400, CaCl2, HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlenzyme1drop
20.2 M1reservoirCaCl2
319-31 %PEG4001reservoir
40.1 MHEPES1reservoirpH7.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 24, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 405031 / Num. obs: 115924 / % possible obs: 98.7 % / Biso Wilson estimate: 10.8 Å2
Reflection shellResolution: 2.05→2.12 Å / % possible all: 98.2
Reflection
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 20 Å / Num. obs: 115876 / % possible obs: 98.7 % / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.135

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FXU

1fxu


Resolution: 2.05→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: PROTEIN WAS CO-CRYSTALLIZED WITH 9PP FROM 19-31% PEG-400 IN 100 MM HEPES BUFFER, PH 7.25; 100 MM CACL2 PROTEIN WAS MIXED WITH 9PP AT A 1:5 ( PNP TRIMER : INHIBITOR) MOLAR RATIO IN THRE ...Details: PROTEIN WAS CO-CRYSTALLIZED WITH 9PP FROM 19-31% PEG-400 IN 100 MM HEPES BUFFER, PH 7.25; 100 MM CACL2 PROTEIN WAS MIXED WITH 9PP AT A 1:5 ( PNP TRIMER : INHIBITOR) MOLAR RATIO IN THRE PRESENCE OF ORTHOPHOSPHATE AT 1:22 ( PNP TRIMER : ORTHOPHOSPHATE) MOLAR RATIO
RfactorNum. reflection% reflectionSelection details
Rfree0.244 9323 8 %RANDOM
Rwork0.188 ---
all0.189 115876 --
obs-115876 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.8383 Å2 / ksol: 0.378319 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å20 Å2
2---1.26 Å20 Å2
3----2.15 Å2
Refine analyzeLuzzati coordinate error free: 0.28 Å / Luzzati sigma a free: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12850 0 130 1829 14809
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 2.05→2.12 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 1546 8.2 %
Rwork0.206 17286 -
obs-11390 97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3INH.PARAMINH.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0059
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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