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- PDB-3fuc: Recombinant calf purine nucleoside phosphorylase in a binary comp... -

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Basic information

Entry
Database: PDB / ID: 3fuc
TitleRecombinant calf purine nucleoside phosphorylase in a binary complex with multisubstrate analogue inhibitor 9-(5',5'-difluoro-5'-phosphonopentyl)-9-deazaguanine structure in a new space group with one full trimer in the asymmetric unit
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / purine nucleoside phosphorylase / recombinant / glycosyltransferase / 9-deazaguanine / multisubstrate analogue inhibitors / nucleoside-binding / phosphate-binding / binding site / trimer
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-9D9 / AZIDE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBochtler, M. / Breer, K. / Bzowska, A. / Chojnowski, G. / Hashimoto, M. / Hikishima, S. / Narczyk, M. / Wielgus-Kutrowska, B. / Yokomatsu, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: 1.45 A resolution crystal structure of recombinant PNP in complex with a pM multisubstrate analogue inhibitor bearing one feature of the postulated transition state.
Authors: Chojnowski, G. / Breer, K. / Narczyk, M. / Wielgus-Kutrowska, B. / Czapinska, H. / Hashimoto, M. / Hikishima, S. / Yokomatsu, T. / Bochtler, M. / Girstun, A. / Staron, K. / Bzowska, A.
History
DepositionJan 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2016Group: Non-polymer description
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_conn / 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.ptnr2_auth_asym_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.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.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_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
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,18510
Polymers95,0613
Non-polymers1,1247
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-39 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.795, 78.253, 94.901
Angle α, β, γ (deg.)90.00, 97.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-302-

MG

21C-303-

MG

31C-505-

HOH

41C-511-

HOH

51C-516-

HOH

61C-530-

HOH

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Components

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


Mass: 31687.113 Da / Num. of mol.: 3 / Fragment: residues 1-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: NP, PNP / Plasmid: PET-28A+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P55859, purine-nucleoside phosphorylase
#2: Chemical ChemComp-9D9 / [5-(2-amino-4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-1,1-difluoropentyl]phosphonic acid / DFPP-DG


Mass: 336.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H15F2N4O4P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FEATURE OF UNIPROT (PNPH_BOVIN, P55859) SHOWS "CONFLICT" AT THIS POSITION: A -> Q (IN REF. 1)

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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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 33% PEG 400, 0.1M SODIUM AZIDE, 0.1M HEPES, 0.1M MAGNESIUM CHLORIDE, 1% OCTYL BETA-D-GLUCOPYRANOSIDE, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 18, 2007 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.45→10 Å / Num. all: 173360 / Num. obs: 173360 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.082 / Net I/σ(I): 4.4
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 25329 / Rsym value: 0.236 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
MOLREPphasing
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LVU

1lvu


Resolution: 1.45→10 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19933 8787 5.1 %THIN RESIOLUTION SHELLS
Rwork0.17999 ---
all0.18095 173360 --
obs0.18095 173360 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.13 Å2
2---0.26 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6456 0 72 447 6975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227112
X-RAY DIFFRACTIONr_bond_other_d00.026349
X-RAY DIFFRACTIONr_angle_refined_deg1.3862.0059700
X-RAY DIFFRACTIONr_angle_other_deg3.6833.00714763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67423.965343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.148151189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3841554
X-RAY DIFFRACTIONr_chiral_restr0.0930.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028229
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021502
X-RAY DIFFRACTIONr_nbd_refined0.210.21333
X-RAY DIFFRACTIONr_nbd_other0.2460.26192
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23449
X-RAY DIFFRACTIONr_nbtor_other0.1060.23402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2332
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0040.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7821.54359
X-RAY DIFFRACTIONr_mcbond_other01.51787
X-RAY DIFFRACTIONr_mcangle_it1.36927072
X-RAY DIFFRACTIONr_scbond_it2.07132753
X-RAY DIFFRACTIONr_scangle_it3.2644.52624
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.449→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 676 -
Rwork0.215 12059 -
obs-12059 99.1 %

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