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

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Basic information

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


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 / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
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: 2 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
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)312,64738
Polymers309,81712
Non-polymers2,83026
Water19,0421057
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)156,60022
Polymers154,9096
Non-polymers1,69116
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26090 Å2
ΔGint-140 kcal/mol
Surface area43880 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)156,04716
Polymers154,9096
Non-polymers1,13910
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24110 Å2
ΔGint-141 kcal/mol
Surface area44640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.560, 138.998, 318.723
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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


Mass: 25818.105 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

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Non-polymers , 5 types, 1083 molecules

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


Mass: 92.094 Da / Num. of mol.: 20 / 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.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-05Z / 6-benzylthio-2-chloropurine / 2-chloranyl-6-phenylmethylsulfanyl-7H-purine


Mass: 276.745 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9ClN4S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1057 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 12% PEG 8000, Tris-HCl pH 7,0

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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: Feb 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.62 Å / Num. obs: 204075 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Biso Wilson estimate: 36.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.181 / Rrim(I) all: 0.189 / Χ2: 0.727 / Net I/σ(I): 9.79
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
2-2.121.9020.8932293832721322660.6372.00398.6
2.12-2.261.2381.6739863830746307410.841.288100
2.26-2.440.8492.6437866728666286620.9220.883100
2.44-2.680.544.3833694326490264850.9670.562100
2.68-2.990.2958.232866924011240100.9860.307100
2.99-3.450.16914.8326966021302213000.9930.176100
3.45-4.220.09825.5221104218169181630.9960.103100
4.22-5.950.08132.0416649414186141850.9970.085100
5.95-49.620.0635.899673830282630.9990.06399.5

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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: 2→49.62 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2854 1999 0.99 %
Rwork0.2288 200857 -
obs0.2293 202856 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.15 Å2 / Biso mean: 44.8743 Å2 / Biso min: 15.76 Å2
Refinement stepCycle: final / Resolution: 2→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21616 0 180 1057 22853
Biso mean--46.6 40.83 -
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 (%)
2-2.050.43991390.4056139651410498
2.05-2.110.44081410.37231421114352100
2.11-2.170.41411420.35041416114303100
2.17-2.240.33431410.32511423514376100
2.24-2.320.36361420.30141425714399100
2.32-2.410.40311420.29541428714429100
2.41-2.520.37361410.29241426214403100
2.52-2.650.34541420.26761426414406100
2.65-2.820.3141430.25291436414507100
2.82-3.040.3371430.25361434814491100
3.04-3.340.28041440.22971438714531100
3.34-3.830.25791440.20611445314597100
3.83-4.820.21241440.16631462314767100
4.82-49.620.22191510.1751504015191100

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