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- PDB-6g7x: Crystal structure of H. pylori purine nucleoside phosphorylase so... -

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Basic information

Entry
Database: PDB / ID: 6g7x
TitleCrystal structure of H. pylori purine nucleoside phosphorylase soaked in PO4
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsTRANSFERASE / Purine nucleoside phosphorylase / H. pylori
Function / homology
Function and homology information


purine-nucleoside phosphorylase / purine nucleoside catabolic process / 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
IMIDAZOLE / PHOSPHATE ION / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 Å
AuthorsStefanic, Z.
Funding support Croatia, 1items
OrganizationGrant numberCountry
7423 Croatia
CitationJournal: Croatica Chemica Acta / Year: 2018
Title: The Role of Phosphate Binding in Purine Nucleoside Phosphorylase of Helicobacter pylori
Authors: Bosnjakovic, M. / Lescic Asler, I. / Stefanic, Z.
History
DepositionApr 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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

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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)157,06735
Polymers154,9096
Non-polymers2,15929
Water18,5011027
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29070 Å2
ΔGint-82 kcal/mol
Surface area43130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.320, 91.490, 93.410
Angle α, β, γ (deg.)90.000, 119.900, 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 (strain ATCC 700392 / 26695) (bacteria)
Gene: deoD, HP_1178 / Plasmid: pET21b / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P56463, purine-nucleoside phosphorylase
#2: Chemical...
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1027 / 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: 44.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 mol L-1 imidazole, 40% (w/v) polypropylene glycol (PPG) 400

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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: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→60.64 Å / Num. obs: 133830 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.348 / Num. unique obs: 19209 / CC1/2: 0.936 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F52

6f52


Resolution: 1.762→46.753 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.38
RfactorNum. reflection% reflection
Rfree0.1929 1986 1.48 %
Rwork0.1589 --
obs0.1594 133830 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.07 Å2 / Biso mean: 18.9557 Å2 / Biso min: 5.6 Å2
Refinement stepCycle: final / Resolution: 1.762→46.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 145 1027 11984
Biso mean--30.86 27.16 -
Num. residues----1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611225
X-RAY DIFFRACTIONf_angle_d0.8115096
X-RAY DIFFRACTIONf_chiral_restr0.0521721
X-RAY DIFFRACTIONf_plane_restr0.0051902
X-RAY DIFFRACTIONf_dihedral_angle_d12.4296779
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7618-1.80590.28661270.21079056918396
1.8059-1.85470.22621360.185894109546100
1.8547-1.90930.24641380.176194509588100
1.9093-1.97090.20921400.16893739513100
1.9709-2.04140.24221400.168595129652100
2.0414-2.12310.231430.169393999542100
2.1231-2.21970.22561430.167893989541100
2.2197-2.33680.17561430.163894809623100
2.3368-2.48320.17391420.165393219463100
2.4832-2.67490.17741480.161894789626100
2.6749-2.9440.2341420.165994289570100
2.944-3.36990.18171500.151994799629100
3.3699-4.24530.1651380.138994929630100
4.2453-46.76950.15691560.140795689724100

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