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- PDB-6f4w: Crystal structure of H. pylori purine nucleoside phosphorylase in... -

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Basic information

Entry
Database: PDB / ID: 6f4w
TitleCrystal structure of H. pylori purine nucleoside phosphorylase in complex with formycin A
ComponentsPurine nucleoside phosphorylase DeoD-type
KeywordsHYDROLASE / Purine nucleoside phosphorylase / H. pylori / formycin A
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
Chem-FMC / Purine nucleoside phosphorylase DeoD-type
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 Å
AuthorsStefanic, Z.
Funding support Croatia, Poland, 3items
OrganizationGrant numberCountry
Croatian Science Founataion7423 Croatia
National Science Center of Poland2015/18/M/NZ1/00776 Poland
Polish Ministry for Science and Higher EducationBST-173300/BF 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
DepositionNov 30, 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)156,51212
Polymers154,9096
Non-polymers1,6036
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24980 Å2
ΔGint-123 kcal/mol
Surface area44140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.051, 84.801, 274.462
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 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: Chemical
ChemComp-FMC / (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol


Mass: 267.241 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 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 PILATUS3 2M / Detector: PIXEL / Date: Sep 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.293→46.081 Å / Num. obs: 66682 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 40.47 Å2 / Rpim(I) all: 0.083 / Rrim(I) all: 0.168 / Rsym value: 0.145 / Net I/av σ(I): 3.598 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2.293-2.423.90.9290.80.5341.0760.92998.6
2.42-2.564.30.541.40.2930.6160.5499.5
2.56-2.744.30.3811.90.2090.4360.38199.7
2.74-2.964.20.2752.60.1540.3160.27599.9
2.96-3.2440.1893.50.1120.2210.18999.5
3.24-3.633.90.1364.60.0810.1590.13699.6
3.63-4.194.20.1055.70.0590.120.10599.7
4.19-5.1340.09860.0570.1140.09899.4
5.13-7.253.70.1025.80.0620.120.10299.5
7.25-46.08140.08860.050.1020.08898.7

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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: 2.293→46.081 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.56
RfactorNum. reflection% reflection
Rfree0.2667 3298 4.96 %
Rwork0.202 --
obs0.2052 66548 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.86 Å2 / Biso mean: 46.0297 Å2 / Biso min: 22.41 Å2
Refinement stepCycle: final / Resolution: 2.293→46.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10812 0 114 422 11348
Biso mean--44.05 43.92 -
Num. residues----1398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811164
X-RAY DIFFRACTIONf_angle_d0.96715043
X-RAY DIFFRACTIONf_chiral_restr0.0541735
X-RAY DIFFRACTIONf_plane_restr0.0061873
X-RAY DIFFRACTIONf_dihedral_angle_d16.076725
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 (%)
2.2933-2.3260.44051220.32722509263196
2.326-2.36080.32431440.3172561270599
2.3608-2.39760.36261500.27326082758100
2.3976-2.4370.35591280.2692602273099
2.437-2.4790.32951410.259125652706100
2.479-2.5240.28711250.25012657278299
2.524-2.57260.32071180.247126112729100
2.5726-2.62510.26761370.23232642277999
2.6251-2.68220.33721320.230825502682100
2.6822-2.74460.32671440.25292648279299
2.7446-2.81320.33921290.242426242753100
2.8132-2.88920.31851380.23932617275599
2.8892-2.97420.29461370.234926322769100
2.9742-3.07020.28721370.228426212758100
3.0702-3.17990.29971390.217726512790100
3.1799-3.30720.32491400.22162625276598
3.3072-3.45770.28631230.205626352758100
3.4577-3.63990.29071440.206226632807100
3.6399-3.86790.22161430.182526452788100
3.8679-4.16630.2271240.16382674279899
4.1663-4.58520.20491450.15022676282199
4.5852-5.24790.24691780.1552662284099
5.2479-6.60870.22331370.19732712284999
6.6087-46.09010.21711430.17322860300399

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