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- PDB-5mx4: Crystal structure of H. pylori purine nucleoside phosphorylase fr... -

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Basic information

Entry
Database: PDB / ID: 5mx4
TitleCrystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate HpPNP-1
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / purine nucleoside phosphorylase / clinical isolate / Helicobacter pylori / dead-end-complex
Function / homology
Function and homology information


uridine phosphorylase / uridine phosphorylase activity / 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
HYPOXANTHINE / PHOSPHATE ION / Uridine phosphorylase
Similarity search - Component
Biological speciesHelicobacter pylori R018c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsStefanic, Z.
Funding support Croatia, 2items
OrganizationGrant numberCountry
Croatian Science Foundation7423 Croatia
FP7/2007-2013, Biostruct-X283570
CitationJournal: Int. J. Biol. Macromol. / Year: 2017
Title: Structural characterization of purine nucleoside phosphorylase from human pathogen Helicobacter pylori.
Authors: Stefanic, Z. / Mikleusevic, G. / Luic, M. / Bzowska, A. / Lescic Asler, I.
History
DepositionJan 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,1348
Polymers154,9036
Non-polymers2312
Water15,403855
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21690 Å2
ΔGint-137 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.190, 129.492, 156.019
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: 25817.096 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Helicobacter pylori R018c (bacteria)
References: UniProt: K2JXG0, purine-nucleoside phosphorylase
#2: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M MgCl2, 0.1M Tris-HCl pH 7.0, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9781 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 2.31→48.768 Å / Num. obs: 67351 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 28.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.083 / Χ2: 0.987 / Net I/σ(I): 16.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.31-2.450.2885.31104420.9480.31798
2.45-2.620.2047.47100310.9740.224100
2.62-2.820.1599.8193520.9810.17699.9
2.82-3.090.11213.686400.9890.12599.9
3.09-3.460.07819.678320.9950.08699.9
3.46-3.990.06326.2869030.9950.0799.2
3.99-4.880.04832.459230.9970.05399.6
4.88-6.860.04530.4446740.9970.0599.8
6.86-48.7680.03139.8627600.9980.03499.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1k9s

1k9s


Resolution: 2.31→48.768 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.37
RfactorNum. reflection% reflection
Rfree0.24 3312 4.92 %
Rwork0.1799 --
obs0.1828 67351 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.8 Å2 / Biso mean: 30.8692 Å2 / Biso min: 11.1 Å2
Refinement stepCycle: final / Resolution: 2.31→48.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 15 855 11682
Biso mean--31.97 31.97 -
Num. residues----1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811038
X-RAY DIFFRACTIONf_angle_d0.93914865
X-RAY DIFFRACTIONf_chiral_restr0.0531709
X-RAY DIFFRACTIONf_plane_restr0.0051868
X-RAY DIFFRACTIONf_dihedral_angle_d16.036712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2998-2.33260.3971730.28632575274899
2.3326-2.36740.31831280.24926682796100
2.3674-2.40440.28071200.209126462766100
2.4044-2.44380.29931290.195426402769100
2.4438-2.4860.26341280.185826522780100
2.486-2.53120.25071340.190326422776100
2.5312-2.57990.27821550.193826112766100
2.5799-2.63250.26151360.186626602796100
2.6325-2.68980.28041430.188626352778100
2.6898-2.75230.28451320.186426702802100
2.7523-2.82120.26441510.188726222773100
2.8212-2.89740.25571340.193926452779100
2.8974-2.98270.2471180.189727052823100
2.9827-3.07890.25361230.181926752798100
3.0789-3.18890.22021250.178126552780100
3.1889-3.31660.22461310.180926852816100
3.3166-3.46750.23051380.184526622800100
3.4675-3.65030.27211600.19572626278699
3.6503-3.87890.27431440.22772636278098
3.8789-4.17820.19041400.15262671281199
4.1782-4.59840.17591390.134327062845100
4.5984-5.26310.1851460.128127042850100
5.2631-6.62840.22621390.163427592898100
6.6284-48.79270.2011460.162128893035100

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