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- PDB-5i3c: Crystal structure of E.coli purine nucleoside phosphorylase with ... -

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Basic information

Entry
Database: PDB / ID: 5i3c
TitleCrystal structure of E.coli purine nucleoside phosphorylase with acycloguanosine
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / complex
Function / homology
Function and homology information


purine-nucleoside phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
9-HYROXYETHOXYMETHYLGUANINE / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsTimofeev, V.I. / Abramchik, Y.A. / Esipov, R.S. / Kuranova, I.P.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with acyclovir.
Authors: Timofeev, V.I. / Zhukhlistova, N.E. / Abramchik, Y.A. / Muravieva, T.I. / Esipov, R.S. / Kuranova, I.P.
History
DepositionFeb 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 11, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,32111
Polymers77,1653
Non-polymers1,1568
Water2,414134
1
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules

A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,64222
Polymers154,3306
Non-polymers2,31216
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area26510 Å2
ΔGint-252 kcal/mol
Surface area45540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.030, 120.030, 238.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-425-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase DeoD-type / PNP


Mass: 25721.633 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Gene: deoD, EcE24377A_4983 / Production host: Escherichia coli (E. coli)
References: UniProt: A7ZVS7, purine-nucleoside phosphorylase
#2: Chemical ChemComp-AC2 / 9-HYROXYETHOXYMETHYLGUANINE


Mass: 225.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H11N5O3 / Comment: medication, antivirus*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 294 K / Method: liquid diffusion / Details: ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. obs: 44040 / % possible obs: 98.66 % / Redundancy: 5.55 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.004
Reflection shellResolution: 2.32→2.45 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.66 / % possible all: 93.72

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RJ2

4rj2


Resolution: 2.32→29.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.456 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.189 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21664 2152 4.9 %RANDOM
Rwork0.17613 ---
obs0.17806 41823 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.911 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.32→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5391 0 73 134 5598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195621
X-RAY DIFFRACTIONr_bond_other_d0.0020.025402
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9827582
X-RAY DIFFRACTIONr_angle_other_deg0.97312409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0055712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92823.734233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51415958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1451537
X-RAY DIFFRACTIONr_chiral_restr0.0870.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026325
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021256
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0223.1072851
X-RAY DIFFRACTIONr_mcbond_other2.0213.1062850
X-RAY DIFFRACTIONr_mcangle_it3.4194.6513562
X-RAY DIFFRACTIONr_mcangle_other3.4184.6523563
X-RAY DIFFRACTIONr_scbond_it2.2123.4972769
X-RAY DIFFRACTIONr_scbond_other2.2083.4922749
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7245.1253991
X-RAY DIFFRACTIONr_long_range_B_refined5.6524.6986154
X-RAY DIFFRACTIONr_long_range_B_other5.63924.6976131
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 127 -
Rwork0.227 2759 -
obs--90.1 %

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