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- PDB-7ooy: Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-... -

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Basic information

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


purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / 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
6-benzylthio-2-chloropurine / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 28, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77512
Polymers51,6362
Non-polymers1,13910
Water6,395355
1
A: Purine nucleoside phosphorylase DeoD-type
B: Purine nucleoside phosphorylase DeoD-type
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)158,32436
Polymers154,9096
Non-polymers3,41630
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area29730 Å2
ΔGint-158 kcal/mol
Surface area42110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.591, 113.591, 113.591
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

21B-560-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 25818.105 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 365 molecules

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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-05Z / 6-benzylthio-2-chloropurine / 2-chloranyl-6-phenylmethylsulfanyl-7H-purine


Mass: 276.745 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9ClN4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 13% PEG 8000, 0.1M Tris pH 7.6, 0.02M MgCl2

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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: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.373 Å / Num. obs: 38789 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 20.88 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.317 / Rrim(I) all: 0.332 / Χ2: 0.747 / Net I/σ(I): 7.82
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
1.9-2.011.9731.2765646619761820.512.07399.8
2.01-2.151.2792.0565922586458630.731.34100
2.15-2.320.8973.0363445542454240.8510.938100
2.32-2.550.6823.9957504500950090.9060.714100
2.55-2.850.4515.948859456845680.9540.474100
2.85-3.280.24310.5345584402740270.9870.254100
3.28-4.020.12919.2240264345234520.9960.135100
4.02-5.660.08825.4428775269026900.9980.093100
5.66-46.3730.08927.1917607158015740.9990.09499.6

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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: 1.9→40.16 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 1996 5.15 %
Rwork0.1662 36757 -
obs0.1683 38753 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.5 Å2 / Biso mean: 23.6827 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 1.9→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 79 356 4039
Biso mean--28.98 31.42 -
Num. residues----466
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 (%)
1.9-1.950.3261390.2712566270599
1.95-20.29471440.241126292773100
2-2.060.29911440.233225782722100
2.06-2.120.27151400.211726002740100
2.12-2.20.24331420.204326162758100
2.2-2.290.24051430.190426182761100
2.29-2.390.19491350.183925782713100
2.39-2.520.22241450.173926252770100
2.52-2.680.22761420.176126292771100
2.68-2.880.22521460.165926152761100
2.88-3.170.20031420.153226392781100
3.17-3.630.19741420.138626352777100
3.63-4.570.12131440.120926712815100
4.58-40.160.18671480.146827582906100

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