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- PDB-6f5i: Crystal structure of H. pylori purine nucleoside phosphorylase -

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Basic information

Entry
Database: PDB / ID: 6f5i
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 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
METHANOL / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,03710
Polymers154,9096
Non-polymers1284
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22260 Å2
ΔGint-136 kcal/mol
Surface area45080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.332, 59.609, 136.440
Angle α, β, γ (deg.)90.000, 102.150, 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(DE3) (bacteria)
References: UniProt: P56463, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
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: 2.298→133.384 Å / Num. obs: 60022 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rpim(I) all: 0.101 / Rrim(I) all: 0.253 / Rsym value: 0.231 / Net I/av σ(I): 3.14 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.3-2.426.30.8050.90.3470.8790.80597.9
2.42-2.576.50.72510.3090.7890.725100
2.57-2.756.40.5441.40.2350.5940.544100
2.75-2.9760.441.70.1970.4830.4499.9
2.97-3.255.70.2792.60.1290.3090.27999.9
3.25-3.636.40.18140.0790.1980.181100
3.63-4.26.40.1156.40.0490.1260.115100
4.2-5.1460.0977.50.0430.1070.09799.8
5.14-7.275.70.1285.70.0590.1410.12899.9
7.27-47.4846.60.0689.50.0280.0730.06899.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MX4

5mx4


Resolution: 2.298→44.444 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.16
RfactorNum. reflection% reflection
Rfree0.2523 2996 5 %
Rwork0.1909 --
obs0.194 59917 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.9 Å2 / Biso mean: 23.8795 Å2 / Biso min: 6.06 Å2
Refinement stepCycle: final / Resolution: 2.298→44.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 8 547 11367
Biso mean--25.92 23.99 -
Num. residues----1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811003
X-RAY DIFFRACTIONf_angle_d114804
X-RAY DIFFRACTIONf_chiral_restr0.0541704
X-RAY DIFFRACTIONf_plane_restr0.0051860
X-RAY DIFFRACTIONf_dihedral_angle_d16.2086687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2979-2.33550.33241260.25192492261893
2.3355-2.37580.3251460.229227492895100
2.3758-2.4190.29841230.225826712794100
2.419-2.46550.28971390.225626982837100
2.4655-2.51590.30231430.229127002843100
2.5159-2.57060.34981070.219627572864100
2.5706-2.63030.26881300.215626872817100
2.6303-2.69610.28071360.21727332869100
2.6961-2.7690.27781790.217126482827100
2.769-2.85050.30171650.225527322897100
2.8505-2.94250.30061540.22626682822100
2.9425-3.04760.28511470.219527012848100
3.0476-3.16960.25621680.205726862854100
3.1696-3.31380.25351490.185427122861100
3.3138-3.48840.24681480.174527172865100
3.4884-3.70690.24721490.17327282877100
3.7069-3.9930.20631180.157427472865100
3.993-4.39450.18481310.148327242855100
4.3945-5.02960.20311480.144527492897100
5.0296-6.33380.24741390.190127592898100
6.3338-44.45220.20431510.179328633014100

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