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

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Basic information

Entry
Database: PDB / ID: 7ooz
TitlePurine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-benzyloxo-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-benzyloxo-2-chloropurine / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)53,79624
Polymers51,6362
Non-polymers2,16022
Water5,350297
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)161,38872
Polymers154,9096
Non-polymers6,47966
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 area38670 Å2
ΔGint-202 kcal/mol
Surface area40000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.736, 113.736, 113.736
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-490-

HOH

21B-517-

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 , 6 types, 319 molecules

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


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-05Q / 6-benzyloxo-2-chloropurine / 2-chloranyl-6-phenylmethoxy-7H-purine


Mass: 260.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9ClN4O / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 48.2 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 12% PEG 8000, 0,1 M 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: 1.7→46.433 Å / Num. obs: 104465 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.132 / Χ2: 1.088 / Net I/σ(I): 8.67
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
1.7-1.81.061.267393916972168880.5181.20799.5
1.8-1.930.5972.387080115921159170.7760.679100
1.93-2.080.3374.066247014736147220.9040.38599.9
2.08-2.280.2186.486358413608136070.9620.246100
2.28-2.550.168.615657712325123250.9780.181100
2.55-2.940.10811.94637610834108060.9870.12399.7
2.94-3.60.06919.1442715918091780.9950.078100
3.6-5.070.04926.1831653710070780.9960.05699.7
5.07-46.4330.05326.0917793396539440.9970.0699.5

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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: 1.7→40.21 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 1990 3.68 %
Rwork0.161 52019 -
obs0.162 54009 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.61 Å2 / Biso mean: 23.146 Å2 / Biso min: 9.32 Å2
Refinement stepCycle: final / Resolution: 1.7→40.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 146 305 4055
Biso mean--32.53 32.85 -
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 (%)
1.7-1.740.32571400.2933681382199
1.74-1.790.29171380.247337023840100
1.79-1.840.24531370.212736633800100
1.84-1.90.21541430.186336873830100
1.9-1.970.20021370.172536763813100
1.97-2.050.18821420.168236943836100
2.05-2.140.23691400.175637153855100
2.14-2.250.18521400.156136933833100
2.26-2.40.20021450.160736963841100
2.4-2.580.15611450.155837103855100
2.58-2.840.16971430.157637163859100
2.84-3.250.20611460.139337493895100
3.25-4.10.14651410.135837663907100
4.1-40.210.17651530.153638714024100

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