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- PDB-5lu0: Crystal structure of H. pylori referent strain in complex with PO4 -

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Basic information

Entry
Database: PDB / ID: 5lu0
TitleCrystal structure of H. pylori referent strain in complex with PO4
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / Purine nucleoside phosphorylase / H. pylori
Function / homology
Function and homology information


purine nucleoside metabolic process / purine nucleoside catabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / 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
PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsStefanic, Z.
Funding support Croatia, 1items
OrganizationGrant numberCountry
Croatian science foundation7423 Croatia
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
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Feb 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 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)156,39824
Polymers154,9096
Non-polymers1,48918
Water24,3921354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26490 Å2
ΔGint-111 kcal/mol
Surface area43890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.520, 86.310, 268.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 natural source / Source: (natural) Helicobacter pylori (bacteria)
References: UniProt: I9S9Z7, UniProt: P56463*PLUS, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1354 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Tris, 10 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979771
20.979571
ReflectionResolution: 1.73→134.22 Å / Num. obs: 133010 / % possible obs: 87 % / Redundancy: 11 % / Net I/σ(I): 28.88
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 3.86 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PNP from E. Coli

Resolution: 1.73→134.22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.574 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1391 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.134 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 6228 4.9 %RANDOM
Rwork0.1838 ---
obs0.1859 126978 87.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.41 Å2 / Biso mean: 17.1663 Å2 / Biso min: 4.85 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→134.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 92 1354 12258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911101
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.98114933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72251405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63623.931435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.428152048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7911554
X-RAY DIFFRACTIONr_chiral_restr0.1670.21715
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218012
X-RAY DIFFRACTIONr_mcbond_it1.1561.4235598
X-RAY DIFFRACTIONr_mcangle_it1.8422.1286983
X-RAY DIFFRACTIONr_scbond_it1.6851.6365503
LS refinement shellResolution: 1.729→1.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 504 -
Rwork0.231 9097 -
all-9601 -
obs--90.08 %

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