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- PDB-5iu6: Crystal structure of E.coli purine nucleoside phosphorylase with ... -

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Basic information

Entry
Database: PDB / ID: 5iu6
TitleCrystal structure of E.coli purine nucleoside phosphorylase with 7-deazahypoxanthine
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / complex
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine nucleoside catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / DNA damage response / membrane / identical protein binding / 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
7H-pyrrolo[2,3-d]pyrimidin-4-ol / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 in complex with 7-deazahypoxanthine.
Authors: Timofeev, V.I. / Zhukhlistova, N.E. / Abramchik, Y.A. / Fateev, I.I. / Kostromina, M.A. / Muravieva, T.I. / Esipov, R.S. / Kuranova, I.P.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 2.0Jun 6, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)77,8589
Polymers77,1653
Non-polymers6946
Water2,468137
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)155,71718
Polymers154,3306
Non-polymers1,38712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area22340 Å2
ΔGint-256 kcal/mol
Surface area45740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.370, 120.370, 238.971
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
11A-418-

HOH

21A-422-

HOH

31B-440-

HOH

41C-425-

HOH

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Components

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


Mass: 25721.633 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: deoD, pup, b4384, JW4347 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABP8, purine-nucleoside phosphorylase
#2: Chemical ChemComp-7HX / 7H-pyrrolo[2,3-d]pyrimidin-4-ol


Mass: 135.123 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5N3O
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.24 Å3/Da / Density % sol: 62.02 %
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: 2.51→29.87 Å / Num. obs: 35075 / % possible obs: 98.12 % / Redundancy: 4.47 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.4375
Reflection shellResolution: 2.51→2.65 Å / Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→29.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.928 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R Free: 0.211 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20047 1762 5 %RANDOM
Rwork0.15467 ---
obs0.15701 33258 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.687 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.51→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5391 0 45 137 5573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195545
X-RAY DIFFRACTIONr_bond_other_d0.0020.025366
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9687477
X-RAY DIFFRACTIONr_angle_other_deg0.976312328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67823.707232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45515961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5571537
X-RAY DIFFRACTIONr_chiral_restr0.0820.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026267
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021235
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_it3.1932.5562851
X-RAY DIFFRACTIONr_mcbond_other3.1912.5562850
X-RAY DIFFRACTIONr_mcangle_it4.1643.8293562
X-RAY DIFFRACTIONr_mcangle_other4.1643.8293563
X-RAY DIFFRACTIONr_scbond_it3.9632.9722692
X-RAY DIFFRACTIONr_scbond_other3.9632.9712681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0494.3273896
X-RAY DIFFRACTIONr_long_range_B_refined5.34319.775934
X-RAY DIFFRACTIONr_long_range_B_other5.3219.7625919
X-RAY DIFFRACTIONr_rigid_bond_restr2.601310909
X-RAY DIFFRACTIONr_sphericity_free28.218554
X-RAY DIFFRACTIONr_sphericity_bonded13.106510905
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 114 -
Rwork0.176 2290 -
obs--94.09 %

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