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- PDB-9fxe: D204N mutant of Purine Nucleoside Phosphorylase from E.coli in co... -

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Basic information

Entry
Database: PDB / ID: 9fxe
TitleD204N mutant of 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 phosphorylase activity / purine nucleoside catabolic process / 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: 2.12 Å
AuthorsNarczyk, M. / Stachelska-Wierzchowska, A. / Wierzchowski, J.
Funding support Poland, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher Education (Poland)661-79/2024 Poland
Ministry of Science and Higher Education (Poland)17.610.011-110 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
DepositionJul 1, 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
C: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7059
Polymers77,9433
Non-polymers7626
Water3,153175
1
A: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)157,41018
Polymers155,8866
Non-polymers1,52512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area22660 Å2
ΔGint-170 kcal/mol
Surface area44460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.525, 120.525, 241.206
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
11B-425-

HOH

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Components

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


Mass: 25980.961 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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: Citrate buffer pH 5.2, amonium sulphate 24% 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: 2.12→48.22 Å / Num. obs: 59360 / % possible obs: 97.46 % / Redundancy: 40.3 % / Biso Wilson estimate: 38.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.0455 / Rrim(I) all: 0.299 / Net I/σ(I): 15.24
Reflection shellResolution: 2.12→2.196 Å / Redundancy: 34.5 % / Rmerge(I) obs: 3.43 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 5825 / CC1/2: 0.589 / Rpim(I) all: 0.587 / Rrim(I) all: 3.481 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→48.22 Å / SU ML: 0.2545 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 23.393
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 2794 4.83 %
Rwork0.2044 55112 -
obs0.2058 57906 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.45 Å2
Refinement stepCycle: LAST / Resolution: 2.12→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5388 0 51 175 5614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675527
X-RAY DIFFRACTIONf_angle_d0.8357452
X-RAY DIFFRACTIONf_chiral_restr0.0543842
X-RAY DIFFRACTIONf_plane_restr0.0076959
X-RAY DIFFRACTIONf_dihedral_angle_d14.67981995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.160.36951380.3052778X-RAY DIFFRACTION100
2.16-2.20.33961440.3032760X-RAY DIFFRACTION100
2.2-2.240.35461330.31762479X-RAY DIFFRACTION90.01
2.24-2.280.3975840.42051759X-RAY DIFFRACTION62.84
2.28-2.330.27081500.2482740X-RAY DIFFRACTION100
2.33-2.390.27961280.23562805X-RAY DIFFRACTION100
2.39-2.450.28241340.23022785X-RAY DIFFRACTION100
2.45-2.510.24741630.21762798X-RAY DIFFRACTION100
2.51-2.590.24311330.21262773X-RAY DIFFRACTION100
2.59-2.670.21161540.19272793X-RAY DIFFRACTION100
2.67-2.770.27591460.20472787X-RAY DIFFRACTION99.97
2.77-2.880.2531190.2082851X-RAY DIFFRACTION99.97
2.88-3.010.241350.20182809X-RAY DIFFRACTION100
3.01-3.170.26831630.19642816X-RAY DIFFRACTION100
3.17-3.360.20321530.18972818X-RAY DIFFRACTION99.97
3.36-3.620.19971270.19412854X-RAY DIFFRACTION100
3.62-3.990.26211490.21262759X-RAY DIFFRACTION96.8
3.99-4.570.17671380.15692898X-RAY DIFFRACTION99.93
4.57-5.750.17931390.17922937X-RAY DIFFRACTION99.97
5.75-48.220.22311640.19953113X-RAY DIFFRACTION99.79

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