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- PDB-9fpe: Wild type Purine Nucleoside Phosphorylase from E.coli in complex ... -

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Basic information

Entry
Database: PDB / ID: 9fpe
TitleWild type Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / fluorescent ligand
Function / homology
Function and homology information


purine nucleoside interconversion / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / DNA damage response / identical protein binding / membrane / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsNarczyk, M. / Krystian, M. / Stachelska-Wierzchowska, A. / Wierzchowski, J.
Funding support Poland, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher Education (Poland)17.610.011-110 Poland
Ministry of Science and Higher Education (Poland)661-79/2024 Poland
CitationJournal: Int J Mol Sci / Year: 2024
Title: Interaction of Tri-Cyclic Nucleobase Analogs with Enzymes of Purine Metabolism: Xanthine Oxidase and Purine Nucleoside Phosphorylase.
Authors: Stachelska-Wierzchowska, A. / Narczyk, M. / Wierzchowski, J. / Bzowska, A. / Wielgus-Kutrowska, B.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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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)79,27315
Polymers77,9463
Non-polymers1,32712
Water8,179454
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)158,54530
Polymers155,8926
Non-polymers2,65424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area25570 Å2
ΔGint-239 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.277, 120.277, 239.409
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

21B-435-

HOH

31B-442-

HOH

41B-538-

HOH

51C-514-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 25981.947 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: deoD, pup, b4384, JW4347 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABP8, purine-nucleoside phosphorylase

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Non-polymers , 5 types, 466 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1IEC / N,2,3-etheno-2-aminopurine / 1~{H}-imidazo[2,1-b]purine


Mass: 159.148 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 61.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: Citrate buffer pH 5.2, amonium sulphate 15% w/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.35→48.03 Å / Num. obs: 221855 / % possible obs: 100 % / Redundancy: 40.1 % / Biso Wilson estimate: 22.98 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.054 / Rrim(I) all: 0.246 / Net I/σ(I): 10.2
Reflection shellResolution: 7.4→48.03 Å / Redundancy: 36.3 % / Rmerge(I) obs: 0.046 / Mean I/σ(I) obs: 73 / Num. unique obs: 1611 / CC1/2: 1 / Rpim(I) all: 0.01 / Rrim(I) all: 0.047

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Processing

Software
NameVersionClassification
REFMAC1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→48.03 Å / SU ML: 0.2674 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 26.9299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2128 10585 4.94 %
Rwork0.1959 203617 -
obs0.1967 214202 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.68 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5391 0 84 454 5929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065577
X-RAY DIFFRACTIONf_angle_d0.91517521
X-RAY DIFFRACTIONf_chiral_restr0.0902846
X-RAY DIFFRACTIONf_plane_restr0.0102963
X-RAY DIFFRACTIONf_dihedral_angle_d7.0454774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.46123360.45266876X-RAY DIFFRACTION98.78
1.37-1.380.41013510.41516928X-RAY DIFFRACTION100
1.38-1.40.55873640.52986725X-RAY DIFFRACTION96.92
1.4-1.422.1297192.0587391X-RAY DIFFRACTION5.62
1.42-1.440.56253350.55526551X-RAY DIFFRACTION94.73
1.44-1.450.41493490.38976963X-RAY DIFFRACTION100
1.45-1.480.63433560.63856936X-RAY DIFFRACTION99.99
1.48-1.50.43173570.42026974X-RAY DIFFRACTION100
1.5-1.520.31683550.31486978X-RAY DIFFRACTION100
1.52-1.550.29993480.30066951X-RAY DIFFRACTION100
1.55-1.570.31513510.29096956X-RAY DIFFRACTION99.99
1.57-1.60.29843970.28386957X-RAY DIFFRACTION99.99
1.6-1.630.28183660.27426970X-RAY DIFFRACTION100
1.63-1.670.29023550.27596980X-RAY DIFFRACTION100
1.67-1.70.30473530.2766967X-RAY DIFFRACTION100
1.7-1.740.2593870.25036988X-RAY DIFFRACTION99.99
1.74-1.780.24133730.23496964X-RAY DIFFRACTION100
1.78-1.830.22323460.20817007X-RAY DIFFRACTION100
1.83-1.890.20253750.19557005X-RAY DIFFRACTION100
1.89-1.950.20313990.18286973X-RAY DIFFRACTION100
1.95-2.020.20413560.18457026X-RAY DIFFRACTION99.97
2.02-2.10.19963860.1877012X-RAY DIFFRACTION100
2.1-2.190.1993850.18237048X-RAY DIFFRACTION100
2.19-2.310.18753520.16697067X-RAY DIFFRACTION99.99
2.31-2.450.19573750.17047072X-RAY DIFFRACTION100
2.45-2.640.19473780.1727077X-RAY DIFFRACTION100
2.64-2.910.18543320.17467191X-RAY DIFFRACTION100
2.91-3.330.20313760.17527178X-RAY DIFFRACTION100
3.33-4.20.16854060.15967242X-RAY DIFFRACTION100
4.2-48.030.19733670.17497664X-RAY DIFFRACTION99.91

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