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- PDB-1yr3: Escherichia coli purine nucleoside phosphorylase II, the product ... -

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Basic information

Entry
Database: PDB / ID: 1yr3
TitleEscherichia coli purine nucleoside phosphorylase II, the product of the xapA gene
ComponentsXanthosine phosphorylase
KeywordsTRANSFERASE / purine nucleoside phosphorylase guanine xanthine
Function / homology
Function and homology information


guanosine catabolic process / xanthosine catabolic process / inosine nucleosidase activity / deoxyguanosine catabolic process / NAD+ biosynthetic process via the salvage pathway / deoxyinosine catabolic process / inosine catabolic process / nucleobase-containing small molecule metabolic process / guanosine phosphorylase activity / nucleobase-containing small molecule interconversion ...guanosine catabolic process / xanthosine catabolic process / inosine nucleosidase activity / deoxyguanosine catabolic process / NAD+ biosynthetic process via the salvage pathway / deoxyinosine catabolic process / inosine catabolic process / nucleobase-containing small molecule metabolic process / guanosine phosphorylase activity / nucleobase-containing small molecule interconversion / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / protein hexamerization / identical protein binding / cytoplasm
Similarity search - Function
Xanthosine phosphorylase / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
XANTHINE / Purine nucleoside phosphorylase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDandanell, G. / Szczepanowski, R.H. / Kierdaszuk, B. / Shugar, D. / Bochtler, M.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene
Authors: Dandanell, G. / Szczepanowski, R.H. / Kierdaszuk, B. / Shugar, D. / Bochtler, M.
History
DepositionFeb 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 21, 2015Group: Refinement description
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xanthosine phosphorylase
B: Xanthosine phosphorylase
C: Xanthosine phosphorylase
D: Xanthosine phosphorylase
E: Xanthosine phosphorylase
F: Xanthosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,68318
Polymers179,1946
Non-polymers1,48912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17330 Å2
ΔGint-194 kcal/mol
Surface area54050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.442, 155.232, 93.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsa hexamer with 32 point symmetry that results from the dimerization of trimers

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Components

#1: Protein
Xanthosine phosphorylase / PNP-II / PURINE NUCLEOSIDE PHOSPHORYLASE


Mass: 29865.590 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: xapA, pndA / Plasmid: PGD265 / Production host: Escherichia coli (E. coli) / Strain (production host): GD1524
References: UniProt: P45563, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H4N4O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: TRIS, Li2SO4, PEG4K, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 11, 2002 / Details: Osmic MaxFlux
RadiationMonochromator: Osmic Max Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 35998 / Num. obs: 35998 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 123.4 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 9.9
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1750 / Rsym value: 0.357 / % possible all: 97.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQQ

1yqq


Resolution: 3.2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1781 4.8 %random
Rwork0.249 ---
all0.25 35955 --
obs0.25 35955 97.9 %-
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--14.483 Å20 Å20 Å2
2--11.928 Å20 Å2
3---2.555 Å2
Refinement stepCycle: LAST / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12378 0 96 0 12474

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