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- PDB-6f52: Crystal structure of H. pylori purine nucleoside phosphorylase in... -

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Basic information

Entry
Database: PDB / ID: 6f52
TitleCrystal structure of H. pylori purine nucleoside phosphorylase in complex with PO4 and formycin A
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsHYDROLASE / Purine nucleoside phosphorylase / H. pylori / formycin A
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
Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStefanic, Z.
Funding support Croatia, Poland, 3items
OrganizationGrant numberCountry
Croatian Science Founataion7423 Croatia
National Science Center of Poland2015/18/M/NZ1/00776 Poland
Poland
CitationJournal: FEBS J. / Year: 2018
Title: Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.
Authors: Narczyk, M. / Bertosa, B. / Papa, L. / Vukovic, V. / Lescic Asler, I. / Wielgus-Kutrowska, B. / Bzowska, A. / Luic, M. / Stefanic, Z.
History
DepositionNov 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)154,9096
Polymers154,9096
Non-polymers00
Water13,259736
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20930 Å2
ΔGint-131 kcal/mol
Surface area46140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.617, 64.792, 140.727
Angle α, β, γ (deg.)90.000, 99.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25818.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: deoD, HP_1178 / Plasmid: pET21b / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P56463, purine-nucleoside phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M MgCl2, 0.1M TRIS-HCl, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→47.37 Å / Num. obs: 100026 / % possible obs: 99.35 % / Redundancy: 3.67 % / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.122 / Net I/av σ(I): 5.9131 / Net I/σ(I): 7.6999
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.113.540.8198.06
2.11-2.243.890.4799.9
2.24-2.393.830.3699.82
2.39-2.583.750.2699.75
2.58-2.833.40.1999.58
2.83-3.163.590.1199.52
3.16-3.653.790.0799.02
3.65-4.473.630.0699.08
4.47-6.333.370.0699.4
6.33-47.373.990.0599.62

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALACCP4_3.3.22data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MX4

5mx4


Resolution: 2→47.368 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.88
RfactorNum. reflection% reflection
Rfree0.2465 5021 5.03 %
Rwork0.2053 --
obs0.2074 99788 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.24 Å2 / Biso mean: 37.3796 Å2 / Biso min: 13.77 Å2
Refinement stepCycle: final / Resolution: 2→47.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 0 736 11548
Biso mean---38.51 -
Num. residues----1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811000
X-RAY DIFFRACTIONf_angle_d0.93114806
X-RAY DIFFRACTIONf_chiral_restr0.0531704
X-RAY DIFFRACTIONf_plane_restr0.0051860
X-RAY DIFFRACTIONf_dihedral_angle_d15.3116690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0003-2.0230.36131520.32962915306791
2.023-2.04680.32081700.31433132330299
2.0468-2.07180.35841510.302231753326100
2.0718-2.0980.36021570.28543168332599
2.098-2.12560.32431850.278430983283100
2.1256-2.15480.33511640.277332013365100
2.1548-2.18550.29111780.269731253303100
2.1855-2.21820.32661580.266431753333100
2.2182-2.25280.28131490.259232023351100
2.2528-2.28980.31431640.26213126329099
2.2898-2.32920.29741570.257932073364100
2.3292-2.37160.32571710.253731313302100
2.3716-2.41720.33681710.253931693340100
2.4172-2.46650.27021560.246431963352100
2.4665-2.52020.30191770.23623131330899
2.5202-2.57880.30441680.24113142331099
2.5788-2.64330.27061660.22833138330499
2.6433-2.71470.26771950.23283166336199
2.7147-2.79460.29241590.2343146330599
2.7946-2.88480.29471750.24623129330499
2.8848-2.98790.31561700.22983165333599
2.9879-3.10750.24541660.21483176334299
3.1075-3.24890.24121960.20583124332099
3.2489-3.42010.23381610.20193174333599
3.4201-3.63430.21421400.18613194333499
3.6343-3.91480.21741600.16593155331598
3.9148-4.30860.19491710.15533177334899
4.3086-4.93150.17671870.1383166335399
4.9315-6.21090.20121600.165332553415100
6.2109-47.38120.1751870.155633093496100

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