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

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Basic information

Entry
Database: PDB / ID: 1yqu
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 / NAD+ biosynthetic process via the salvage pathway / deoxyguanosine catabolic process / 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 / NAD+ biosynthetic process via the salvage pathway / deoxyguanosine catabolic process / 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 catabolic process / purine-nucleoside phosphorylase activity / 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
GUANINE / PHOSPHATE ION / Purine nucleoside phosphorylase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 2, 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 1.3Aug 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Xanthosine phosphorylase
B: Xanthosine phosphorylase
C: Xanthosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3359
Polymers89,5973
Non-polymers7386
Water00
1
A: Xanthosine phosphorylase
B: Xanthosine phosphorylase
C: Xanthosine phosphorylase
hetero molecules

A: Xanthosine phosphorylase
B: Xanthosine phosphorylase
C: Xanthosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,67018
Polymers179,1946
Non-polymers1,47712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)71.345, 71.345, 267.537
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
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.: 3
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5N5O

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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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: Tris, PEG4K, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 4, 2002
RadiationMonochromator: triangular monochromator, bent mirror (information from the Web-site)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Num. all: 15055 / Num. obs: 15055 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 11
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1436 / Rsym value: 0.382 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4PNP

4pnp


Resolution: 3.1→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2674 747 random
Rwork0.2451 --
all0.2461 14985 -
obs0.2461 14985 -
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1--5.666 Å2-3.068 Å20 Å2
2---5.666 Å20 Å2
3---11.332 Å2
Refinement stepCycle: LAST / Resolution: 3.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5553 0 48 0 5601

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