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- PDB-2iq5: Unliganded Crystal Structure of the Uridine Phosphorylase from Sa... -

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Basic information

Entry
Database: PDB / ID: 2iq5
TitleUnliganded Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium at 1.90 A Resolution
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / NUCLEOSIDE PHOSPHORYLASE
Function / homology
Function and homology information


nucleotide catabolic process / uridine phosphorylase / nucleoside catabolic process / uridine phosphorylase activity / UMP salvage / cytosol
Similarity search - Function
Uridine phosphorylase / 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
Uridine phosphorylase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTimofeev, V.I. / Dontsova, M.V. / Gabdoulkhakov, A.G. / Pavlyuk, B.P. / Mikhailov, A.M.
CitationJournal: To be Published
Title: Unliganded Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium at 1.90 A Resolution
Authors: Timofeev, V.I. / Dontsova, M.V. / Gabdoulkhakov, A.G. / Lashkov, A.A. / Voelter, V. / Kachalova, G.S. / Pavlyuk, B.P. / Mikhailov, A.M.
History
DepositionOct 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine phosphorylase
B: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)54,0762
Polymers54,0762
Non-polymers00
Water3,153175
1
A: Uridine phosphorylase
B: Uridine phosphorylase

A: Uridine phosphorylase
B: Uridine phosphorylase

A: Uridine phosphorylase
B: Uridine phosphorylase


Theoretical massNumber of molelcules
Total (without water)162,2276
Polymers162,2276
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area15850 Å2
ΔGint-123 kcal/mol
Surface area49390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.660, 151.660, 47.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a hexamer generated from the dimer, which presented in the asymmetric unit.

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Components

#1: Protein Uridine phosphorylase / UrdPase / UPase


Mass: 27037.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: UDP / Plasmid: PBLUESCRIPT IISK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P0A1F6, uridine phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8126
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 15, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 1.9→76.7 Å / Num. obs: 32175 / Redundancy: 2.71 %
Reflection shellResolution: 1.9→1.95 Å

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Processing

SoftwareName: REFMAC / Version: 5.2.0003 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.2 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24693 1592 5 %RANDOM
Rwork0.20141 ---
obs0.2037 30242 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.893 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å2-0.9 Å20 Å2
2---1.79 Å20 Å2
3---2.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 0 175 3723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223603
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9564888
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4785471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70723.759141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63415600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3551525
X-RAY DIFFRACTIONr_chiral_restr0.0810.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022670
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21615
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22461
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 109 -
Rwork0.283 2069 -
obs--96.37 %

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