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- PDB-6f5a: Crystal structure of H. pylori purine nucleoside phosphorylase -

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Basic information

Entry
Database: PDB / ID: 6f5a
TitleCrystal structure of H. pylori purine nucleoside phosphorylase
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsHYDROLASE / Purine nucleoside phosphorylase / H. pylori
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 / 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: 2.201 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
DepositionDec 1, 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

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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


Theoretical massNumber of molelcules
Total (without water)154,9096
Polymers154,9096
Non-polymers00
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20940 Å2
ΔGint-134 kcal/mol
Surface area46110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.748, 65.093, 140.193
Angle α, β, γ (deg.)90.000, 99.620, 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) / Strain: ATCC 700392 / 26695 / 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.: 544 / Source method: isolated from a natural source / Formula: H2O

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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: 49.43 %
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: 2.2→47.38 Å / Num. obs: 75302 / % possible obs: 99.35 % / Redundancy: 3.72 % / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.147 / Net I/av σ(I): 5.3 / Net I/σ(I): 7.3915
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.323.70.92198.26
2.32-2.463.910.6199.97
2.46-2.633.840.4299.9
2.63-2.843.760.3199.85
2.84-3.113.460.2299.7
3.11-3.483.670.1199.66
3.48-4.023.840.0799.22
4.02-4.923.620.0698.06
4.92-6.963.390.0799.29
6.96-47.383.960.0398.9

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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: 2.201→43.296 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.55
RfactorNum. reflection% reflection
Rfree0.2519 3655 4.86 %
Rwork0.2018 --
obs0.2042 75172 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.93 Å2 / Biso mean: 42.9774 Å2 / Biso min: 15.25 Å2
Refinement stepCycle: final / Resolution: 2.201→43.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 0 544 11356
Biso mean---39.41 -
Num. residues----1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810999
X-RAY DIFFRACTIONf_angle_d0.99214804
X-RAY DIFFRACTIONf_chiral_restr0.0531704
X-RAY DIFFRACTIONf_plane_restr0.0051860
X-RAY DIFFRACTIONf_dihedral_angle_d15.7046687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2015-2.23050.37331150.31312548266393
2.2305-2.2610.36931340.29692774290899
2.261-2.29330.34061410.29742705284699
2.2933-2.32750.30311510.273327662917100
2.3275-2.36390.35031360.274927372873100
2.3639-2.40270.33431570.260227522909100
2.4027-2.44410.30881380.260127102848100
2.4441-2.48850.3121270.25128172944100
2.4885-2.53640.32311460.255427392885100
2.5364-2.58810.34391330.251327702903100
2.5881-2.64440.35481160.242727412857100
2.6444-2.70590.30741520.238627822934100
2.7059-2.77360.30661550.24326972852100
2.7736-2.84860.31421530.2427642917100
2.8486-2.93240.28571680.229227282896100
2.9324-3.0270.23851330.22552766289999
3.027-3.13510.32361390.21952744288399
3.1351-3.26060.26651440.225527552899100
3.2606-3.4090.28221440.215927662910100
3.409-3.58860.23061300.194227862916100
3.5886-3.81330.20291370.17982785292299
3.8133-4.10760.21551460.16122712285898
4.1076-4.52050.19561430.14892706284998
4.5205-5.17370.19361470.1512769291698
5.1737-6.51480.22471240.1782820294499
6.5148-43.30410.15911460.14122878302499

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