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- PDB-7op9: Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 2,... -

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Basic information

Entry
Database: PDB / ID: 7op9
TitlePurine nucleoside phosphorylase(DeoD-type) from H. pylori with 2,6-dichloropurine
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / inhibitor / complex
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / 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
2,6-bis(chloranyl)-7H-purine / IMIDAZOLE / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNarczyk, M. / Stefanic, Z.
Funding support Poland, Croatia, 3items
OrganizationGrant numberCountry
Polish National Science Centre2015/18/M/NZ1/00776 Poland
Croatian Science FoundationIP-2013-11-7423, IP-2019-04-6764 Croatia
Ministry of Science and Higher Education (Poland)BST-173300/BF Poland
CitationJournal: J Enzyme Inhib Med Chem / Year: 2022
Title: Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium.
Authors: Narczyk, M. / Wojtys, M.I. / Lescic Asler, I. / Zinic, B. / Luic, M. / Jagusztyn-Krynicka, E.K. / Stefanic, Z. / Bzowska, A.
History
DepositionMay 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
D: Purine nucleoside phosphorylase DeoD-type
E: Purine nucleoside phosphorylase DeoD-type
F: Purine nucleoside phosphorylase DeoD-type
G: Purine nucleoside phosphorylase DeoD-type
H: Purine nucleoside phosphorylase DeoD-type
I: Purine nucleoside phosphorylase DeoD-type
J: Purine nucleoside phosphorylase DeoD-type
K: Purine nucleoside phosphorylase DeoD-type
L: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,85149
Polymers310,39312
Non-polymers3,45837
Water47,9382661
1
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
C: Purine nucleoside phosphorylase DeoD-type
D: Purine nucleoside phosphorylase DeoD-type
E: Purine nucleoside phosphorylase DeoD-type
F: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,96025
Polymers155,1976
Non-polymers1,76319
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24270 Å2
ΔGint-160 kcal/mol
Surface area43890 Å2
MethodPISA
2
G: Purine nucleoside phosphorylase DeoD-type
H: Purine nucleoside phosphorylase DeoD-type
I: Purine nucleoside phosphorylase DeoD-type
J: Purine nucleoside phosphorylase DeoD-type
K: Purine nucleoside phosphorylase DeoD-type
L: Purine nucleoside phosphorylase DeoD-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,89124
Polymers155,1976
Non-polymers1,69418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24210 Å2
ΔGint-162 kcal/mol
Surface area43780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.419, 93.428, 95.459
Angle α, β, γ (deg.)81.910, 79.350, 60.090
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 25866.104 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: deoD, HP_1178 / Production host: Escherichia coli (E. coli)
References: UniProt: P56463, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-06K / 2,6-bis(chloranyl)-7H-purine / 2,6-dichloropurine


Mass: 189.002 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H2Cl2N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2661 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M imidazole pH 7,0, PPG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→46.831 Å / Num. obs: 773378 / % possible obs: 87.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.087 / Χ2: 1.021 / Net I/σ(I): 6.59
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.590.3431.391624581425721177420.7920.48582.6
1.59-1.70.2212.231640791339101189550.8880.31388.8
1.7-1.840.1543.271446051245341078240.9370.21886.6
1.84-2.010.0975.331449171145001043300.9710.13791.1
2.01-2.250.0687.83129782103658939330.9840.09690.6
2.25-2.590.0549.8410578891582795480.9890.07786.9
2.59-3.180.04512.869557277276696090.9910.06390.1
3.18-4.480.0416.196953059666518230.990.05786.9
4.48-46.8310.03817.063973833000296140.9920.05489.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F4X

6f4x


Resolution: 1.5→42.59 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 2013 0.48 %
Rwork0.1733 415551 -
obs0.1734 417564 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.72 Å2 / Biso mean: 19.0956 Å2 / Biso min: 4.8 Å2
Refinement stepCycle: final / Resolution: 1.5→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21660 0 209 2661 24530
Biso mean--18.19 27.95 -
Num. residues----2796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.37131170.316263852650284
1.54-1.580.33211510.2679283522850391
1.58-1.620.24411400.237293752951594
1.62-1.680.22071460.2171298442999095
1.68-1.740.24061460.2019297402988695
1.74-1.810.23771470.193298372998496
1.81-1.890.18861340.1794301043023896
1.89-1.990.24041460.174302553040196
1.99-2.110.20871510.1675302293038097
2.11-2.280.18161460.1686302433038996
2.28-2.510.19131440.1727303163046097
2.51-2.870.18881460.1663304383058497
2.87-3.610.17381460.1554301563030296
3.61-42.590.1521530.1417302773043097

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